Don't Fit Anywhere
by Trekkiewhoviansmurf
Summary: There was a stow-away aboard the SS Botany Bay. Doesn't follow the story exactly. Not sure where it is going. Read to find out. May change parts. Focuses on Khan and an OC. Might have some overly descriptive parts. Some bad language because I stuck to the story as closely as possible in some parts.
1. Chapter 1

This story isn't going to follow the film perfectly but hopefully it will be good anyway. Reviews welcomed.

* * *

"Final stage of awakening."

"Everything normal."

"Core temperature rising."

"Blood pressure normal."

"No problems."

"Reactions normal."

The girl lying in the cryo-tube made a little sound at the back of her throat and turned her head slightly. The room was full of doctors, who all froze when she moved. When she made no further movements the doctors continued with their work. She was the last of 74 people found in cryo-tubes on an old sleeper ship. Unlike the others there was no evidence of genetic modification and she looked like a teenager. One of the doctors lifted her out of the tube and placed her on a bed. Her eyelids flickered slightly, as though she was trying to open them, then a hypospray was pressed against her neck and she relaxed completely.

* * *

There we go. Please give me feedback. Hopefully I will explain things later


	2. Chapter 2

The guards pushed a teenaged girl into the large cell.  
She looked scared. She had pale skin, long dark blonde hair and grey-blue eyes.  
It was obvious that she was scared of the guards but she didn't seem to trust  
the people watching her distrustfully. All of them had the same look of  
wariness. The guards seemed oblivious to the tension. "Another relic for you to  
look after, Khan." One of them goaded. Khan ignored the remark, more interested  
in inspecting the newcomer. She was tall but unremarkable in every other way as  
far as he could see. The guards moved away from the barred door and Khan moved  
towards the girl.

"Name?" He demanded in a cold voice.

"Sophia Young." She said softly. Her voice was low and hollow.

"When were you born?"

"1981." Sophia's eyes flickered from one face to another, memorising them

"Are you one of us?"

The first proper emotion showed on her face. She looked confused. "Who is  
'us'?"

"We were called, in your time, 'Augments'" He moved closer to her and she took  
an automatic step away.

"I…you're…" She paused, obviously thinking about something. "No. No, I'm not."  
Khan's lip curled slightly in dislike.

"Stay away from us." He turned away from her and the others followed his lead  
and ignored her completely.

Sophia sat against one of the walls until it was time for dinner and joined the  
end of the line, knowing that she wasn't wanted. The others talked softly  
amongst themselves while she listened and pretended not to be. There was a call  
of 'lights out' and all the others started getting into their beds. When she  
could tell where all of them were sleeping, Sophia chose a bed on the edge of  
the group. Khan made his way over to her. "Follow me." He ordered, not giving  
her time to object. She was led to the furthest bed from the group, closest to  
the door. "You will sleep here."

"Why?" She asked, hurt at his complete and utter rejection of her.

"Because we don't want to have to be near your kind. The humans from your time  
were weaker even than the ones of this time." Khan spun on his heel and glided  
away from her before she could object. While watching the augments she had seen  
that their movements were far smoother and more graceful than normal people's.  
None of them seemed surprised by their leader's actions.

Khan was the first created of them so he became the natural leader, even though  
some where older than he was. He was one of the very first of them meaning that  
he was one of the most changed as the scientists were still seeing how far they  
could take their experiments. His hatred of humans was greater than most as  
well.


	3. Chapter 3

Over the days which followed it became evident that  
none of the augments had any interest in spending any time with Sophia. She  
didn't mind too much because she had always sort solitude and not company.  
Every day she would be taken out of the cell. None of the augments knew why  
and, although some were curious, never asked. One day she was returned later  
than usual. None of the others questioned the change, although most noticed  
that she went straight to bed upon returning and didn't bother to go for  
dinner. One of the women was concerned about her. She walked over to the girl,  
ignoring the glances she got, and saw that she was shaking. "Sophia." She said  
softly. Sophia looked up suddenly, having not realised anyone was close to her.  
She wiped her eyes quickly, not wanting anyone to know she had been crying.  
"What's wrong?"

"I…they…" She stuttered, tears filling her eyes. She started crying and buried  
her face in her pillow. Gently the woman put a hand on her shoulder. Sophia  
shied away automatically and the woman moved closer. She lay on the bed beside  
Sophia and put her arms around the crying child. Sophia curled up next to her,  
shaking and crying.

"Anna, what are you doing?" Khan asked in a low voice. Sophia had fallen asleep  
still curled up in Anna's arms.

"Looking after a child." Anna retorted.

"Leave her. She is only human."

Anna shook her head in disgust. "That is the attitude which landed us in this  
place. This child has done nothing wrong. She is innocent. Her own people will  
not accept her because she is weaker than they are or they don't trust her.  
There is no reason for us to treat her as badly." Khan watched her with a look  
of slight amusement.

"You really think that she won't turn on us the moment it suits her better." He  
mused.

"She won't if we treat her better than they do. She might be useful to us in  
the future."

The next day began as usual and seemed like it was going to continue that way  
until the guards came to take Sophia. She was sitting against her bed, staring  
at her lap, when they opened the door and moved over to her. "Up." One of them  
ordered with his usual arrogance. When Sophia didn't move he grasp her arm to  
pull her up. She lashed out with her other hand in a fist. It caught him in the  
side of the head and he released her but the others were already closing in.  
One man took hold of each of her arms and tried to pull her up but she  
resisted. She cried out in pain when one of the men twisted her arm cruelly.  
The struggle and accompanying shouts had drawn the attention of all the others  
in the area. One of the guards dragged Sophia towards him and got an arm around  
her waist. She shouted more loudly and struck the man across the face. He hung  
on grimly, heaving her towards the door. One of the other guards twisted her  
arm up behind her back and she kicked out wildly. The man holding her had obviously  
had enough and slammed her head against the corner of one of the beds.  
Immediately she went completely limp and the guards carried her out.

* * *

I like to think that some of the augments have a softer side and they aren't really the baddies. Although they are manipulative.

School starts tomorrow so I might not be able to upload every day but I will try to do something every few days

Thank you to the people who have commented, it really makes me happy to know that you are enjoying it.


	4. Chapter 4

It was late when Sophia was returned to the cell. All of the others, accept one, were asleep. She was crying, as quietly as possible. Khan listened as her footsteps moved around the edge of the room, quick and quiet. Silently he rose and followed her. She entered the brightly lit toilets. Khan listened as she started sob, taking great heaving breathes. Carefully he looked around the corner and saw her sitting against the wall with her legs drawn up to her chest and her arms wrapped around them. She was trembling all over and had her eyes shut. Suddenly she seemed to throw herself into one of the cubicles and Khan heard the sound of retching. Still staying silent he moved so he could see her again. Sophia had no idea he was there until he pulled her hair out of her way and put a hand on her back, making soothing circles. Through the thin material of the top he could feel how clammy she was and felt a sudden, unexpected, stab of pity.

Once the vomiting had stopped she sat back, leaning against Khan for support, still crying and shaking more than ever. He held her gently for a few minutes before getting her a glass of water and wiping her face with a damp towel. Neither of them said a word, partial because that would have meant that Khan would have found himself in a situation where he had to explain his actions but mostly because Sophia was in no state to form coherent thoughts let alone sentences. It was obvious that she had seen something or something had been done to her which had upset her greatly. Khan wondered vaguely if there was anything anyone could show him to make him have such a severe reaction. He sat with her for a long time, until her trembling as almost unnoticeable and her breathing controlled. She was half asleep when he picked her up carefully and carried her over to her bed, pulling the blanket over her gently. He tried to move away but Sophia's hand stopped him. "Thank you." She murmured. Khan froze, unsure what to do. She let go of him and closed her eyes to save him from having to find something to say.

The next day began as though the day before hadn't happened. Sophia didn't speak to anyone and Khan ignored her as if he hadn't looked after her the night before. She sat on the floor, leaning against her bed and staring at nothing. Although it wasn't obvious she was in fact listening to the conversations around her. She knew something was going on but she couldn't work out what it was. Again the cell door opened and Sophia shrank down slightly, knowing they were coming for her. She waited for them to order her up and with them. The first one caught sight of her. "Get up." He ordered. Sophia glanced at him quickly then ignored him again. He nodded to one of the people next to him who moved up to her. Sophia looked up, surprised, when another man moved into his way. "What do you want from her?" Khan asked. No-one made a sound for several seconds.  
"That is not your concern." The man who seemed to be in charge answered.  
"It is my concern because she under my protection. If you want to talk to her I want to know what it is about."  
"This is a private matter. Leave us alone." Sophia was watching silently, not certain what was going on.  
Her eyes flicked between the different people. "I'm afraid that she is under my protection and therefore it is my concern. What do you want from her?"  
"Information." He answered illusively.  
"They want information about what you're planning." Sophia informed Khan. "And they want to know any weaknesses." The eyes of the man in charge flicked to Sophia as she spoke.  
"Be quiet." He ordered.  
"Leave her alone." Khan moved in front of her as she stood up. Sophia stayed behind him, knowing that he was a lot more likely to beat people in a fight. "She isn't going with you."  
"Alright then." He nodded to his men again and they left slowly, watching the augments carefully.

The augments went very quiet after the men left. They seemed to be listening to what was happening although Sophia couldn't hear a thing. She watched them for as they stayed silent for several minutes. They all started moving at the same time. Khan took Sophia's arm gently and pulled her towards the back of the cell. She went without fighting him. "What did they do to you?"  
"Why are you doing this?" She asked, ignoring his question.  
"Because I believe that you are more than you say and that they are less than they want to be." Sophia contemplated his answer for a few moments.  
"That really isn't a proper answer."  
"I still need to know what they did to you." Sophia fell very quiet. "Please, it could be important." He spoke more softly.  
"They showed me things. What they would do to me if I didn't give the answers they wanted. And I didn't give them the answers. They showed me other people who hadn't answered them. It wasn't nice." She didn't look at Khan as she spoke.  
He was silent for a few moments. "Stay back here. We are about to have company." He strode away, occasionally speaking to someone.

Something rolled past the cell door and Sophia had the presents of mind to duck. There was a bright flash and a loud bang and several shouts of alarm. Moments later dozens of people rushed in. They all had large guns and were wearing full body armour, including helmets with tinted visors. Sophia stared at them, ears ringing. Most of the augments seemed to be unaffected by the stun grenade and were facing the assault team. For about half a second everyone stayed completely still. Then fighting exploded. The guns were too big to be used as guns so they used them to batter the augments. Khan moved between people, throwing well positioned punches but there were a lot more of the people in the assault team than there were augments. There was a momentary lull in the fighting and Khan looked around. He saw Sophia backing away from a man. The man swung a punch but she jumped out of the way and threw one of her own. She swung a kick back and he was stumbled. She punched him again and he fell. She looked surprised that he had fallen so easily. Without thinking Khan hit the man approaching him and spun away, watching Sophia again. The next person to attack her also fell, in a very short time.

Khan found himself plunged back into the middle of the fighting and lost track of Sophia. He was slightly distracted by what he had seen. She had been fighting in a very calm way, acting completely unlike herself. As far as he was able to tell she was just as surprised at her ability to fight as he was. She wasn't as strong as the augments but she was certainly as clever. A particularly had punch found its way through his defence and Khan focused on the fighting. They were losing. Sheer weight of numbers was felling the augments at an alarming rate. They were being knocked out and handcuffed one after another. There was a loud scream of pain and Khan spun around to see Sophia on the floor with her left arm cradled in her right, obviously broken. She curled up when one of the people kicked her. The others around her started to beat her up. "STOP!" Someone shouted. Amazingly almost everyone froze. "You are not able to win this fight. Surrender now and you will not be hurt further." It was one of the assault team speaking. He was holding a handgun to Sophia's head. She stayed absolutely still.

For several seconds you could have heard a pin drop. Khan made a tiny movement and they all surrendered. Within ten seconds all of them were handcuffed and being lead out of the cell. Khan watched, showing no emotions as far as the guards could tell. Sophia however could see that he was worried and angry. His face was tense and his eyes flicked from one place to another. They rested on her as she was dragged out of the room, still clutching her arm.

* * *

Finally got the next part up. I think Khan has a soft side we don't get to see in the film so I put it in here. Please review.

I've been thinking about putting some chapter names in but I can't come up with any. Any suggestions welcomed.


	5. Chapter 5

Sophia was dragged down corridor to a small cell with a bed set into the wall. She stumbled when the soldier shoved her but didn't fall, although the sharp movement hurt her arm. She sat against the wall breathing slowly to help control the pain. There was a loud bang from down the corridor and she saw several soldiers walking past the door. Several of them glanced in and threw her dirty looks. Sophia didn't react so she didn't provoke them. A few minutes later a woman walked into sight slowly. She looked into each of the cells she passed. She stopped outside Sophia's cell and smiled at her. She looked tense and stressed. "Are you hurt?" She asked. Sophia nodded silently, not sure what she was up to. "Where?"  
"My arm."  
"Can I see it? I'm a doctor." Sophia nodded again and the doctor opened the door and went in. Quickly she knelt beside her and pulled a large bag off her shoulder. Opening it, she withdrew a scanner and ran it over her arm, not touching it. Sophia took the opportunity to study the woman in greater detail. Her hair, which at first glance was black, was greying slightly and pulled back into a loose bun. She frowned at the readings and like up at Sophia. "Your arm I brown but it is a clean break so I can fix it easily."

The doctor started pulling out instruments and Sophia watched, interested in the changes to treatment in the last hundred or so years since she was put into stasis. "I need to align the bones before I can start to heal them. It's going to hurt a bit."  
"You mean a lot don't you." Sophia said with a wry smile. The doctor smiled slightly and took hold of the two parts of her arm which should have been one.

There was a loud cry of pain as the two bones were moved into the right place. The doctor ran the scanner over the break again. After several calming breathes Sophia opened her eyes again. "Ow." She grumbled and the doctor raised and eye brow at her. Sophia wondered if anyone had a sense of humour or if she had just been unlucky with the people she had talked to. The pain was easing as the doctor worked and Sophia was quite happy to just sit there. She wondered where the augments were and if any of them had been hurt. She thought that they would probably be fine but she would have liked some sort of confirmation of it. Suddenly the cell door was soaked open and Sophia jumped, regretting it when pain shot through the half healed bones.  
"What are you doing?" Khan growled, pushing the doctor away from Sophia.  
"She was healing my arm, Khan." Sophia said loudly before things could get any worse. Then several guards entered the room. They appeared to have been chasing Khan. A man wearing an admiral's uniform followed them into the room.

Sophia shrank away from him slightly and Khan stood, recognising her reaction as one of fear. "Who are you?" He demanded.  
"I am the man in charge of this facility and I expect you to stop attacking my people."  
"And I expect you to leave my people alone."  
"You don't seem to have grasped the situation, despite your fabled intellect. I am in charge here and if you don't do what I want you, or one of your 'people', will be hurt."  
"Well, if you want your 'facility' intact, which I assume you do, you will give me what I want and not hurt any of my people." Sophia felt that Khan was more in charge than the man who appeared to be contemplating something. He seemed more of a politician than someone in charge of a jail. She watched him carefully, trying to ignore the nagging fear.  
"We might be able to arrange something to your liking." He said, carefully not making any promises. "First I need to ask you some questions. Is the girl under your protection?" He asked. The doctor moved back to Sophia.  
"She is." He said succinctly.  
"Why?"  
"I believe there is more to her than meets the eye." Sophia stayed still, afraid to draw attention to herself. They were obviously both trying to be the 'alpha male' and neither wanted to back down.

"What more is there to her?" The admiral asked. Khan didn't respond. "Maybe augments do have an idea of what compassion is after all." Sophia noticed the slight change in Khan's posture but the others didn't. The doctor had finished mending her arm and she ducked out of the room. The admiral eyed Khan, who stood unnaturally still. "So, what am I to do with you? And this girl?" He added. Sophia moved further behind Khan, conscious that the conversation could turn nasty very quickly. "I know what I'm going to do to the others, assuming you behave."

"If you want to survive intact you will let me and my crew go." Khan threatened in a low voice.

"And what about the girl." The admiral asked.

"She is part of my crew." Khan lied smoothly. Sophia knew that the admiral wouldn't fall for such a transparent lie, particularly as she had told him the truth.

"No she isn't. We know the truth, don't we Sophia." Sophia didn't look at him. "Why don't you tell Khan the truth? He ought to know." Khan's eyes flickered to Sophia. "Tell him now and we won't have to make you."

Sophia shuddered at the idea of being made to tell them, particularly after the last time. "I stowed away aboard your ship before you all boarded. Once you were all frozen I froze myself." She didn't look up as she spoke.

"Why did you want to leave?" Khan asked, not sure why anyone from that time would want to leave Earth on a ship with augments.

"I grew up surrounded by augments and the scientists were going to experiment on me when the rebellions started. No-one would have trusted me on Earth." Khan suspected that she was hiding something but didn't press the matter.

"So, do you still want the girl?" The admiral asked.

Khan turned to him. "As I told you before, Admiral Marcus, everyone on that ship was part of my crew." Sophia was shocked that he was still protecting her.

Admiral Marcus fixed Khan with a steely look. "Your crew will all be refrozen and you will work for me. The girl will be kept unfrozen to ensure your complete co-operation." Khan's eyes narrowed slightly. The admiral and his security guards left swiftly.

* * *

I don't think Khan likes Marcus. Thank you to for the review. They are always welcomed *hint hint*. I'm sorry if I don't upload for a while but the teachers seem to hate us at the moment, particularly maths. I'll try to upload soon. :)


	6. Chapter 6

Sophia was cold. It seemed to her that the people in charge of the prison had deliberately turned the temperature down. She was sat on the floor with her legs pulled up to her chest hoping the temperature would rise in the near future. Khan was sitting on the bed, apparently deep in thought and she really didn't want to disturb him because she was still scared of him. Finally he seemed to waken from his thoughts, make Sophia wonder if he had actually been meditating. He looked around the room and his eyes fixed on her. "You're cold." He stated calmly.

Sophia shrugged. "A little." She admitted, not wanting him to know the truth.

"Come here." He instructed. She got up slowly and walked over to him. Khan could tell she was scared and wasn't surprised. Very gently he pulled her down onto the bed next to him. He was surprised by just how cold she was. He lay her down on the bed and pulled the blanket over her. Then he lay down as well. She tensed slightly as his arm snaked out and pulled her closer but he was so much warmer than she was that she didn't mind. It wasn't long before Sophia was asleep and Khan was left to wonder why he was being so soft with her.

Sophia didn't wake up when Admiral Marcus came back. He smiled disturbingly happily at the sight. "You really do have a soft spot for her." He mused. Khan resisted throwing something at the man only because there wasn't anything for him to throw. "You crew is now cryogenically frozen. You will be helping us and she will stay here."

"What do you want me to do?" Khan asked. He knew that he had no choice.

"I believe that there is a war coming. You are going to help us win it." Khan raised an eyebrow. "Or," Marcus added. "Your crew will die and the girl will be hurt." Khan made no answer, showing  
Marcus he had won. "Once we have an alias for you, you will begin." Again Khan gave no answer.

Marcus left and Khan looked down at Sophia. She looked a lot younger in sleep than she did awake. She looked a lot like one of the children who had met when he was younger. An awful lot like the girl who had once hidden from bullies behind him. He wondered if fate was playing a cruel trick on him. Gently he shook Sophia awake and told her what was going on. She accepted it without comment. "Sophia, where did you grow up?" Khan asked after a few minutes.

She smiled slightly, he had finally made the connection. "On the corridor above you. Room 96."

"You were one of the little kids who were going to be changed when you were older." She nodded. "You were bullied."

"Not after you helped me but I knew that the normal humans would turn on people like me before too long, just because of fear." She smiled slightly. "I have a question now." Khan sighed and Sophia ignored it. "What did you mean when you said you thought that there was something more to me to Marcus?"

"I meant that I saw you fighting and there is definitely something you aren't telling me." Sophia bit her lip and Khan knew she was thinking. "What is it?" He prompted.

"I'm not entirely un-augmented." She admitted. "The doctors fiddled with my brain just a few weeks before we left on the Botany Bay. I'm still kind of getting used to it." She didn't look at Khan.

"Interesting." Was all he said for some time. Sophia frowned at him. "That is, no doubt, why you were good at fighting." Sophia shook her head. She didn't understand how he could accept that sort of information so easily.

* * *

I'm not entirely convinced by this chapter but I couldn't think of a better was of doing it. Khan is being soft again and Marcus has noticed. Do you want more information about their past?

Thank you to Guest Jassie, , twobrothers135 and lina for reviewing.

Guest Jassie - yes, you can translate it into German and put it up. Please tell me how it does. Ich spreche eine kleine Deutsch. But not enough to translate it.

Thank you to everyone for reading, I will try to update asap.


	7. Chapter 7

The next morning Admiral Marcus came back. Both Khan and Sophia were sitting against the wall. They stood as he, and several security guards, entered the small cell. "Bring Khan and take the girl away."

"Where is she going?" Khan asked, moving in front of her protectively.

"To somewhere more permanent. You will be allowed to see her if you behave."

Khan looked like he was going to argue but Sophia stopped him. "It's alright Khan. It's more than just me you need to worry about at the moment." She moved out from behind him and towards the security guards. Khan caught her arm and stopped her.

"Are you sure about this?"

"No, but I'm doing it anyway." She pulled away from him and he let her go. Two security guards took hold of her arms and led her away. Khan watched her go without showing any emotions. She glanced back at him as she turned the corner.

The next day Khan was given a complete new identity and moved to a new set of rooms. He heard nothing of her. The day after Admiral Marcus, with three security guards, escorted Khan to a small office attached to a far larger room with multiple desks and several larger tables. It was explained to Khan that he would be in charge of a large group of the brightest minds in Starfleet. He didn't complain about it, although he did raise an eyebrow. "You will help us make the most advanced ships and weapons possible. You will not fight us if you want your crew to survive." Khan made no response as he looked around the small room. "You will start working with your team in two weeks. Within that time you will be given free range within this building and access to all the information you might need to get up to date with everything which has happened since you were frozen."

"Will I be allowed to edit my team as I see fit?" He asked, deliberately using the same words as the admiral used.

"To some extent." The admiral said cautiously.

"Do you have any guide lines as to what you want to be created?"

"A ship with advanced warp capability, weaponry and anything else which will make it a better warship. There are some designs being finalised. You will be expected follow them as far as possible without compromising your own designs."

It only took a week for Khan to gather the information necessary to the project. After that he dug into the history of Section 31. It was very informative. By the end of the two weeks he understood more about how the politics of the time worked than any other man possibly could.

Khan stood on a stage in front of nearly two hundred people. They were sitting in rows with holographic projectors set into the arms of the chairs. "My name is John Harrison." All the people fell silent. "I will be leading you in this project. If any of you believe that you are unable to work without correcting mistakes you make before you hand you contributions in you should leave now. I do not accept mistakes and I do not praise success. If you are incompetent you will be kicked out. Anyone who wants to leave should do so now." No-one left. Khan pressed a button and the projectors came to life. They showed plans for star ships and weapons. Whispers spread through the rooms and Khan noted who talked and who didn't. It was easy to work who was useful and who wouldn't be. The quieter ones were looking at the schematics, fascinated.

Khan went back to his office and watched the people going to the desks with stacks of padds containing information. They started working slowly, often talking to the people around them. Khan sat at his desk and started working. He couldn't help wondering what the point was to what he was doing. It all seemed very routine and simple.

* * *

It may be a while before I update again. My dad had an accident and came off the road this evening. He was the only one in the car and is fine apart from some minor cuts and bruises but I am fairly shaken up. I wanted to get this up but it may be a while before family life gets back to normal (being the oldest of four means I will have to help look after the little ones [even if one is my twin sister]). Sorry for the delay but I don't cope with bad things well. Nothing like this has ever happened to someone so close to me.

Thanks go to the people who reviewed. It helped me smile a lot. :)


	8. Chapter 8

Sophia sat in her room. She wanted to know if Khan was alright but no-one would talk to her. She had a couple of padds with books on them. She had read the books and had nothing else to do. After a few moments looking at the door she found that it was impossible to open from the inside without a key card. She was bored of waiting for something to happen but she wasn't sure that she would like what happened. It had been two weeks since she had been taken to the rooms.

After a week of work Khan had a plan. He was going to get his crew out of there as soon as he could. It wasn't hard for him to find the weak points in the security of Section 31. The days began to blur together. He worked on the assignments he was given quickly and concentrated on putting his plan together. Occasionally he would wonder what had become of Sophia but, as far as Khan was concerned, she was expendable. He might have known her once but she wasn't really part of his family and she wasn't really an augment. Khan decided that he would save her if he could but he would not risk his family for her. He wondered how much she trusted him, if she was expecting him to find a way to save her. But most of the time he focused on saving his people.

Sophia spent a lot of her time reading. One of the security guards had taken pity on her and given her some more books. She found there was a lot of history she was missing and the guard had shown her how she could access a library of books from the padd. The stories she read made more sense now that she actually knew what Starfleet and the Federation was. The aliens fascinated her. She often thought about what Khan might be doing. She suspected his intelligence and brutality were being exploited by Admiral Marcus. She had lost track of the date. It had been weeks since she'd been out of the rooms she was locked in.

One day, Sophia wasn't sure which day, Admiral Marcus and two security guards came entered her rooms. As soon as she saw the admiral she stood up, weary of what was to come. "Come with me." Marcus ordered. For half a second Sophia considered disobeying his order but dismissed the idea because she didn't know what he might want. She was led along corridors to a large room. Her eyes widened when she realised that it was filled with cryotubes. It was Khan's crew. "Wait here." Marcus ordered again. He left, one of the guards went with him and the other stayed. Slowly, Sophia approached the nearest tube. A young man was lying peacefully in it. She recognised him from when they were all in one cell together. She moved between the tubes, looking at the sleeping faces. The guard didn't seem to mind her moving among them. They all seemed a lot less dangerous when they were frozen. She turned as the door opened.

Admiral Marcus and half a dozen guards escorted Khan into the room. His eyes fixed onto Sophia. She was standing at the far end of the room, amidst his family. She smiled widely when she saw him. Khan watched as she half ran towards him and flung her arms around his neck. Carefully he put his arms around her, not wanting to hurt her but not entirely convinced by the idea of her hugging him in front of the admiral. Carefully he extracted himself from her arms. "Are you alright?" She nodded, looking at all the security.

"What's going on?" She asked. Khan noticed that she was staying very close to him. It was apparent that she didn't trust Marcus as far as she could throw him.

"That is something I would also like to know." Khan turned to look at Marcus for an explanation. Suddenly, Sophia cried out in surprise. Khan spun around to see a security guard holding her and pressing a phaser into her neck. She looked terrified.

"You have a choice, Khan. Either you will co-operate or you whole crew and Sophia will die." Marcus said. One of the guards was holding a hypospray. He advanced slowly, weary of Khan, and pressed it against the augment's neck. For several seconds nothing happened. Then Khan blinked and swayed slightly. Two of the guards grabbed him and a third punched him in the face. Sophia shouted for them to stop but they didn't. In his weakened state Khan couldn't fight them at all.

After almost a minute Marcus stopped them. "You have been looking for a way to get you crew out of here. For this half of you crew will die."

"No." Sophia shouted, struggling harder than ever.

Marcus looked at her. "Why shouldn't I?" He asked her.

"They haven't done anything wrong. They're defenceless. You can't just go around killing people." She looked desperately at the guards but they didn't say anything.

"And what should I do to ensure Khan doesn't try this again?" He asked. Sophia opened her mouth to speak but no sound came out. "Maybe I should kill you instead."

For a moment Sophia didn't say anything. "Maybe you should." She looked terrified. "It would be better to kill one person than eighty four." She looked Marcus straight in the eye. Khan couldn't understand why she was defending people she barely knew. Particularly after seeing what happened in the eugenics wars.

"I think I know what I'll do." Marcus said, glancing at Khan. "I'm not going to kill you, Sophia." He stroked her cheek and she jerked her head away. He turned to Khan who was barely able to stand. "Sophia will be used a test subject for some of our new weapons and twelve of your crew will die. Be grateful it isn't more." He nodded to the security guards not holding Khan or Sophia and they moved between the tubes. Sophia started shouting and begging on behalf of his crew while Khan could only watch as twelve of the cryotubes were turned off.

They were forced to watch as the augments died. Not even they could survive being woken like that. For a brief time each of them was conscious and Khan was saw their eyes asking why he wasn't saving them. Why they were dying. What had gone wrong. Tears streamed down Sophia's face but Khan showed no emotions. It wasn't until he was alone, after the guards had finished attacking him again, that he allowed himself to cry for his family.

Sophia wasn't taken back to her rooms. She was taken to a small cell and strapped into what appeared to be a dentist's chair. Marcus was with her, reminding her that if she fought he could kill more of Khan's crew. After several minutes two doctors came in and started to put monitors on her. Admiral Marcus watched from the wall. Once the doctors had finished a security guard came in. Sophia glowered at him, recognising him from the room with the cryotubes. He was holding something not dissimilar to a light sabre from Star Wars, except it was all silver and not as long. The security guard was smiling sinisterly at her. "Start on her arm." One of the doctors said. The guard pressed the weapon against Sophia's arm and she screamed as what felt like electricity shot through her body. The doctors seemed very excited by the results.

After an hour the doctors had all the information they needed apparently. Sophia was crying silently and shaking. Her skin was prickling from contact with the weapon and her muscles ached from being so tense. She thought it was over but several more doctors entered the room. She realised that there probably weren't a lot of test subjects for this sort of testing.

Sophia was dragged back to her rooms in just her underwear. She was too weak to walk. She'd lot all track of time and didn't really care. It was days since she'd seen Khan and Marcus had decided that they shouldn't just tests new weapons on her but also to see what methods were most likely to break a person. Sophia curled up on the floor, shaking with cold, and soon fell asleep. She had been kept awake the whole time and given no food and little water. She knew it was just to make sure Khan didn't try to escape but it didn't fell like that. After a few hours she heard the door open and someone walked in. They lifted her into bed and she fell asleep again. After another few hours the person came back. Sophia looked at him and realised that it was the guard who had given her the new books. He tried to persuade her to eat but she just wanted to sleep.

* * *

I am going to upload again tomorrow since it has been a long time since my last upload. I would have uploaded sooner but we had relatives over today and yesterday I had loads of homework and Doctor Who came out, I am thinking of writing a Doctor Who fanfic. I also turned 17 on Thursday and got my provisional driving licence and the DVD of Star Trek Into Darkness, so I ought to be able to stick fairly closely to the story.


	9. Chapter 9

The next day Admiral Marcus was alerted to the fact she wasn't getting any better. He looked in on her and sent several security guards to get Khan and left. As soon as Khan saw Sophia he recognised the symptoms. Several of his crew had been tortured for extended periods and they tended to react in the same way. Very gently he shook her awake. "Sophia, wake up. You need to eat." She looked at him and a tear ran down her cheek. Very gently he helped her sit up. When Khan saw the state she was in he felt a terrible rage. There wasn't a square inch of skin which wasn't bruised or broken. Sophia whimpered in pain as Khan sat her up against the wall. Quickly he grabbed a soft jumper out of her drawers and helped her into it. Then he made her eat the meal which had been left on her desk. She was half asleep but Khan insisted on checking the cuts for infection. Part way through she fell asleep and he laid her on the bed and pulled the blanket over her.

Over the next few days Khan looked after her. She slept most of the time but he was always there when she woke up. He made certain that she had everything she needed. He was grateful to her for protecting his crew. He did notice that she healed fast than a normal human and wondered why since she had only told him that her brain was augmented. After a few days she stopped jumping at every sound and she could look after herself.

Khan watched Sophia as she slept. He hadn't slept much since he had been called to look after her and was starting to feel it. Sophia whimpered in her sleep and turned over. Khan recognised it as a sign that she was having a nightmare and he shook her awake gently. She screamed and sat bolt upright, looking around for someone who wasn't there. She slumped back into her pillows and sighed heavily. She closed her eyes. "Khan, will you…I mean…I was hoping you'd…" She looked at him and he sighed and slipped into the bed next to her. She snuggled up close to him with her head on his chest and fell asleep very quickly. Khan stroked her hair softly until he too drifted off.

Sophia didn't have any more nightmares that night but she woke alone. She guessed that Marcus had wanted his best engineer back. She slid out of bed and found some clothes before heading into the bathroom. After a shower she dressed again and lay back on her bed. She found that she was tired all the time and just wanted to go back to sleep. She also knew that she needed to get back to normal sleep patterns. For several hours she sat with her back against the wall and one of the padds in her hand and completely failed to read anything. She had the first page of Dante's Inferno on the screen of the device but she could have told anyone what the first word was even. Every time she tried to read she started thinking about what happened.

Sophia was woken from her reverie by the door opening. Khan entered, frowning when he saw her sitting on the floor rather than on a chair or in bed. "You should be resting." He stated. She shrugged and turned off the display. It wasn't as though she was actually using it. Khan picked her up and she gave a little shriek of surprise. He dumped her on the bed and took the padd out of her limp hand. "You need to rest, even if you don't want to."

"It isn't that I don't want to. I can't. There are only so many hours I can lie here staring at the ceiling. Anyway, I'm not as fragile as you think."

Khan was getting irritated by her. "You need to rest. You may not be tired but you still ought to rest. You've been through a lot and sleeping will help you sort it out."  
"You mean dreaming." She muttered.

"Sophia." Khan warned.

"Khan." She mimicked, smiling slightly. "Where were you?"

"I was called back to work. The Admiral doesn't like delays. I pointed out that he was the cause of this one."

"Is that why you were beaten up?" Khan looked at her sharply. "There's a little bit of blood in your hairline and your uniform is rumpled oddly." He went over to the mirror and removed the blood and straitened his uniform. He turned back and sat on the edge of her bed.

"How do you feel?"

"Fine. Actually, I'm hungry." She frowned slightly.

"It's very early. I'm sure that breakfast isn't too far away though."

* * *

Khan being sweet again. Can anyone think of chapter titles? Send me any ideas please.


	10. Chapter 10

The weeks which followed we dull and repetitive for Sophia, although she did her best not to let Khan know in case he worried. He visited her most days. Sophia was fascinated by every advance in everything. She pestered him for information about the Federation most of the time, although she had enough tact to avoid Starfleet. Khan spent most of his time working but he didn't seem in the least tired. She did worry that the security guards were hurting him more often than ever.

One day Khan came in looking smug. His face never showed much emotion but she could tell what he felt. "I know that you are bored here. I've talked to the Admiral and he has agreed that you can be my assistant."

"You mean I actually get to do something?" She grinned. A flicker of amusement crossed Khan's face.

Several days later Sophia started working with Khan. There were a few odd looks from the team of people working for Khan but they knew by then not to ask. At the beginning Sophia spent most of her time organising what was going on. She found that there wasn't much logic to the order they were working on the ship which was to be dubbed the USS Vengeance. She didn't voice her distaste at the name. As time went on she started to work on designing the ship itself. She would have enjoyed it if she hadn't known about Marcus' plan to start a war with the Klingons.

The longer she worked with Khan the more she suspected that he was up to something. He was always last to finish in the evening and first in in the mornings. When she asked him what he was doing he claimed it was something she knew it wasn't. A couple of times she had caught him flicking to a different document but he never told her what it was. Sophia was worried that he was working on something to save his crew but didn't trust her enough to tell her.

About year after being woken up Khan disappeared. Sophia got to his office and found Marcus and several security guards waiting there. She was immediately taken back down to a cell. An hour later Marcus came down. "Where is he?" Sophia shrugged. "If you don't want trouble you will answer my questions."

"I don't know where he is."

For the next few days she was locked in the cell. No-one gave her food or water or paid any attention to her. By the time Marcus came back she was exhausted and weak. She did her best to sit up but even that was too much of a strain. A hand supported her head and a glass was pressed to her lips. She drank gratefully. It took her a long time to realise that Marcus was the one helping her. "Where is he?" The Admiral asked very softly.

"I don't know." She rasped. "He wouldn't tell me anything."

Marcus bent down so his face was close to hers. "Do you know anything which might be useful?" He asked. She shook her head. Sophia closed her eyes.


	11. Chapter 11

The next time she woke up she felt an awful lot better. There was a drip leading into her arm and she appeared to be in a sickbay. She noted with some amusement that there were restraints around her wrists so she couldn't go anywhere. There was no-one in sight and Sophia wasn't sure if she wanted to attract attention or not. Someone entered the room and the lights got an awful lot brighter. She squinted, trying to see who it was. "Oh good, you're awake." A horribly bright voice said. "How do you feel?"

"Rubbish." She grumbled.

"You'll feel better in a few hours. I just need to get the doctor." She was half way out of the door before she had finished the sentence.

A hand covered Sophia's mouth and she tried to bite it. "Stop." A voice ordered. She stopped, recognising Khan's voice. "Stay quiet." He said, removing his hand and moving into her line of sight. "Don't ask questions. Marcus is looking for me. My crew is undoubtedly dead. You must find a way to escape here as soon as you can. In two days this place will be destroyed. Do you understand?" She nodded slowly. "Whatever happens, do not get on board the Vengeance."

"Do you think you could loosen the straps?" Sophia asked, already trying to work out a way to escape. He loosened them and slipped back to wherever he had come from as the door opened again.

A doctor and the nurse came back. "How do you feel?" The doctor asked. She seemed a little young to be a doctor but she wasn't going to comment seeing as she was involved in an organisation which wasn't supposed to exist except in myth. After several very long minutes the doctor and nurse left, apparently deciding that she would be fine. Sophia closed her eyes for a minute, pretending to sleep. Once she suspected no-one was about to come in she slipped her wrists out of the restraints. When she realised how short the hospital gown she was wearing was she raised an eyebrow. In one of the cupboards there were some clothes. They were Starfleet uniform with blue strips. Sophia decided that she would claim to be a nurse if she needed to. The uniform fit well, suspiciously well.

As she left the room she picked up a padd and pretended to be reading something on it while walking quickly. She hoped no-one would notice I wasn't meant to be there. Sophia was amazed that she was able to walk out of one of the highest security buildings in the world without being stopped at all. Sophia also had all sorts of interesting specifications on the padd. She walked further and further away from the building, not really knowing where she was going. Suddenly a hand grabbed her wrist and she tried to scream. Another hand covered her mouth and she lashed out. Her arm was twisted up behind her back and she was slammed against the wall. "Must this happen every time we meet?" Sophia relaxed. Khan released her arm and looked her up and down. "You escaped quickly." He stated calmly.

"You wouldn't believe how easy it is to hide in a Starfleet uniform. No-one looks past the colour and the fact that I appeared busy." She smiled slightly. "Hidden in plain sight."

"You are going to need to lie low for a while." He said. "I have rented a flat you can stay in. It's a little way from here."

"What are you going to do?" Sophia asked suspiciously. She didn't trust him not to do something rash. He turned away and didn't answer. "Khan, you need to think about what you are doing. If you do something stupid Starfleet will come after you."

He didn't respond for a long time. Sophia wondered if she had gone too far. "I will avenge my family." He said softly.

"Khan, I…"

"We should go." He cut in, starting to walk away. Sophia sighed and followed him.

* * *

I might not be able to upload for a while. The end of term is coming up and we have loads to do - on top of sixth form work. We have Christmas dinner and entertainment, activities, work teachers want in before the holiday, etc. I had a sixth form award dinner tonight so I didn't get home until after 9 and I don't normally get home until 6:30. Anyway, I will try to upload on the weekend but no promises. If I don't upload for a while I will make sure the next chapter is longer.

Thank you to everyone who has reviewed. It is one of the best parts of the day for me (that tells you how much of a life I have.)


	12. Chapter 12

He led her further away from Section 31 and to a flat. It was small and obviously unused. Sophia looked through the cupboards in the kitchen as soon as she had changed into jeans and a t-shirt. She frowned slightly, trying to remember what she needed for each recipe. She ended up making a stir-fry. Khan came into the kitchen just as she was finishing the cooking. "Do you want some?" She asked.

"I have work to do." He answered shortly.

"Let me rephrase that. You need to eat, so sit down. Even augments need food." Khan looked slightly shocked at her audacity but sat as she served the food. She put a plate down in front of him and grabbed cutlery before sitting down herself.

Khan studied Sophia as they ate. She kept biting her lip and frowning. "What is wrong?" Khan asked when they had both finished eating. Sophia looked up, surprised.

"Nothing, just thinking." Khan watched her, waiting for her to expand. She sighed. "I'm worried that you're going to do something stupid." Khan raised an eyebrow. "You want revenge and you're going to go after Marcus. But you won't just go after Marcus, you'll go after a target which will upset Marcus and be too big for you to handle."

"I will kill Marcus." He growled. "And I will destroy Starfleet." Sophia sighed heavily.

"And how do you intend to do that?"

"Everything is in place." He said somewhat cryptically. Sophia watched him. "You will be safe here."

"I'm not worried about me. Anyway, I can help you. I don't think that Marcus should get away with murder. I just wanted you to think about what you're about to do."

"I don't need help."

"But help would be helpful." Sophia picked up the plates and put them in the dishwasher. Khan frowned at her back but she started to wash up rather than looking at him.

"You cannot help me with this."

"I can but you won't let me." She corrected him.

"Sophia." He warned.

"Alright, alright. But I am right." She heard him walk out of the room and smiled. He couldn't argue with her.

Sophia was in her room when Khan found her. She was lying on her back, staring at the ceiling but sat up as soon as her entered. "Sophia, why do you want to help?" He asked without any preamble.

"Because it is the right thing to do." She smiled slightly. "Also, I owe Marcus for what he did to me."

"You need to stay here. You could be the only one of us left if things don't go to plan."

"But…" She began. Khan interrupted her.

"If things don't go to plan you can tell someone through legal channels and you will be safe."

"Are you concerned about me?" Sophia was genuinely surprised.

"You are part of my family." He said.

"Which means the people Marcus killed were part of my family too. I can help."

"No."

"At least tell me what happened to you so I can report it properly. I don't think I have a very believable story." Khan looked at her suspiciously but began to explain what happened to him.

From Khan's explanation and the digging she had done in Section 31's data bases she had several suspicions which wouldn't be hard to confirm. Under two days later there was an explosion at Section 31. Khan had told her that he wouldn't be back after that morning so she started her own plans. When she heard about the shooting at Starfleet she knew who it was and she knew that Khan would have disappeared. Sophia spent about five minutes considering her plan, or telling herself she was. She had known what she was going to do since the moment she heard what had happened with Khan.

Sophia watched the people get onto the shuttle. She saw Captain James T. Kirk and Doctor McCoy board, followed by Carol Marcus. She recognised her from her time in Section 31. She hoped she wouldn't be recognised or there would be trouble. "Doctor McCoy." She called, rushing up to him. He turned. "Doctor McCoy, I'm Ensign Young. I've been assigned to your team." He frowned.

"I didn't request an extra nurse." He looked at her again. "How old are you?"

"Eighteen, sir. I know I look younger." She smiled at him as though it was a common comment. "These are my transfer orders." She handed him a padd, still smiling. He glanced at it and then back at her.

"Ensign Aurora Young." She nodded, smiling again while watching Carol doing almost the same thing through the shuttle door with Kirk. "Well, everything seems in order. I hope you know more about medicine than the last person I accepted onto my team." She smiled at the comment and followed him towards the shuttle. They sat behind Kirk and Spock as Carol took her place and Kirk told McCoy to leave him alone.

Sophia went to the quarters she had been given and changed into the ridiculously short Starfleet uniform. She quite liked the colour and but hated the slight heel to the boots. Who could run in heels? She checked herself in the mirror and reported to the med bay. It was a long way but she didn't mind walking.

She chewed her lip as she waited to hear anything about their mission. When Kirk announced that they were going to capture Khan rather than kill him she was so glad she almost started to cry. She had seen the torpedoes being loaded on board and she knew what they were carrying. As soon as she saw them she had started to make plans to get Khan's crew out. She wouldn't let anyone else die if she could help it. McCoy had everyone in med bay doing mundane tasks which had to be done. It seemed like he was preparing for a crisis. Considering Kirk's record she wouldn't have been surprised if that was the case.

Suddenly the ship lurched to a halt. Sophia stumbled and looked around. She suspected that foul play was involved in the sudden stop. She wondered if it was Khan or Marcus who damaged the ship. It only took a couple of seconds for her to realise that the Captain would be on his way to Kronos very soon. No-one was watching as she slipped out of med bay and started towards the shuttle bay. She heard the message from Sulu to the shuttle bay and frowned. Kirk was walking towards the shuttle. Sophia ducked out of sight.

There was nowhere to hide on the shuttle so she doubled back and started up to the bridge. McCoy saw her enter the bridge and frowned. "Is anyone up here hurt, Doctor?" She asked. She had had the presence of mind to take a med kit with her. "I heard that the Enterprise bridge crew weren't good at coming down to med bay."

"Everyone's fine at the moment. But stay up here. There's plenty of time yet." He was frowning slightly. Sophia wondered why he was so pessimistic. A few very tense minutes passed as they waited for word from the shuttle. Kirk's voice came over the comm. "Mr Sulu, I think we found our man. You let him know you mean business."

"Aye, Captain."

Sulu didn't look nervous as he opened as channel. "Attention, John Harrison." He paused for a moment. "This is Captain Hikaru Sulu of the U.S.S. Enterprise. A shuttle of highly trained officers is on its way to your location. If you do not surrender to them immediately, I will unleash the entire payload of advanced long-range torpedoes currently locked onto your location. You have two minutes to confirm your compliance. Refusal to do so will result in your obliteration. If you test me, you will fail." He closed the channel. Sophia thought that it could have done without some of the theatrics but she didn't say anything. McCoy on the other hand seemed rather impressed.

"Mr Sulu, remind me never to piss you off." He said.

Khan heard the message and his blood ran cold. If Marcus had given the torpedoes to the Enterprise, his crew would still be inside. He searched through the weapons he had accumulated, deciding what he would need. He heard the first shots from the Klingons and changed which weapons he was choosing.

Sophia wanted to pace but she couldn't. There was the sound of weapons fire and the link broke. "What happened? Where's their signal?" Sulu asked.

A woman replied. "It cut out. I'm working to get them back." Sophia suspected that they had just been the victims of a Klingon attack.

Khan listened to the high-speed chase. He saw them go between the two buildings, bouncing off one then the other. He sprinted to catch up. There would be no way to get his crew if the people on that shuttle were dead, and they would be if the Klingons got them.

Khan listened as the ships settled, still too far away. There was silence, or the sounds were too quiet for even him to hear. He sped up. There was a cry from a woman and he saw them. Khan shot the Klingon and the woman grabbed the knife and stabbed him. Kirk was the first out of the shuttle, already shooting. The Klingons retaliated fast. Khan continued to shoot. The humans ran for cover and he shot at one of the ships in mid-air. It wheeled away. A couple of Klingons got close and he used the weapons to knock them away. He hadn't felt this alive since Marcus had woken him. The humans were holding their own pretty well. But they would have been dead without him. More Klingons dropped from their ships. Kirk was on the floor. Khan considered leaving him to die but the crew of the Enterprise followed orders better than their captain. He shot the man standing over the Captain, who seemed surprised. Kirk turned to watch him as two of his crew helped him up. Khan brought down another ship while the humans took cover, always the defensive strategy. Khan pulled his mask down to see more easily and spotted Kirk staring in disbelief. He ran and jumped of the platform, shooting one Klingon and throwing a knife into another's throat. Adrenaline pumped through his body as the body count rose. Suddenly there was no-one else to fight.

Khan picked up a gun and aimed it at the humans huddled against the wall. One of them aim a gun at him. "Stand down." Kirk yelled.

Khan ignored him. "How many torpedoes?"

"Stand down!" He shouted again. Khan shot the gun out of the man's hands, noting his pointed ears.

"The torpedoes, the weapons you threatened me with in your message. How many are there?" He demanded.

Kirk and the woman stared at him in silence but the other man answered. "Seventy-two."

Khan looked up at him. He had been right. After a few moments he threw the gun down. "I surrender." The man with pointed ears picked the gun up quickly and aimed it at him. Kirk got up slowly.

"On behalf of Christopher Pike, my friend, I accept your surrender." He sounded out of breath. Kirk half turned away then swung a punch. And another, another. He kept hitting him. Khan barely reacted. The other two watched, apparently not sure what to do.

"Captain!" The woman yelled eventually.

"Captain." Khan said softly, realising who was before him.

"Cuff him." He ordered.

Khan was escorted along the corridors of the Enterprise but several security officers. He looked around, spotting Carol Marcus. "Bone, meet me in the brig." Kirk ordered into his communicator.

"Be right there." The man replied. The security officer didn't stop walking. He was taken to the brig. On the way there he spotted Sophia. She glanced at him, winked and looked away. Good to know there was one person on his side on the ship, even if she had ignored his instructions.

* * *

Finally meeting some new character. I decided that I would upload over 2,000 words as over 2,000 people have viewed this story. I never know when I will be able to upload again, hopefully Saturday or Sunday, but my little sister has some friends over for the weekend and I've been kicked out of my room because hers is too small for them. Wednesday is the last day of term so I should be able to finish the story soon.

Thank you to everyone who has favourited or reviewed, I love reading comments.


	13. Chapter 13

"Sounds like we have a superman on board." Khan heard the sound of 'Bones' voice as the Captain, Doctor and man with pointed ears walked into the brig.

"You tell me." Kirk said. The doctor moved the ring into the middle of the screen separating him from the rest of the ship and opened it.

"Put your arm through the hole. I'm gonna take a blood sample." The doctor instructed, pulling out medical instrument. Khan walked to the screen and pulled up his sleeve. He put his arm through the hole and let the doctor take blood, while looking at Kirk.

"Why aren't we moving, Captain?" He asked. Silence greeted him. "An unexpected malfunction, perhaps in your warp core conveniently stranding you on the edge of Klingon space?" The doctor looked up as he spoke.

"How the hell do you know that?" The doctor asked.

"Bones." Kirk seemed to be warning him from getting drawn into the conversation.

"I think you'd find my insight valuable, Captain." Bones finished drawing blood and Khan took his arm back through the hole.

"We good?" Kirk asked

"Yeah."

"Let me know what you find."

"Ignore me and you will get everyone on this ship killed." Khan warned as the three people walked away.

The Captain stopped. "Captain, I believe he will only attempt to manipulate you. I would not recommend engaging the prisoner further."

"Give me a minute." Kirk said and the man left. Kirk walked back, he seemed to be fighting the urge to start shouting again. "Let me explain what's happening here. You are a criminal. I watched you murder innocent men and woman." His voice was rising. "I was authorised to end you! And the only reason you are still alive is because I am allowing it. So shut. Your. Mouth."

"Oh, Captain," Khan said in a perfectly level voice, "are you going to punch me again, over and over till your arm weakens? Clearly you want to, so tell me, why did you allow me to live?" He pretended to be really asking.

"We all make mistakes."

Khan shook his head. "No. I surrendered to you because, despite your attempts to convince me otherwise, you seem to have a conscience, Mr Kirk. If you did not then it would be impossible to convince you of the truth. 23-17-46-11. Coordinates not far from Earth. If you want to know why I did what I did, go and take a look."

"Give me one reason why I should listen to you?" Kirk was suspicious.

Khan was speaking almost before Kirk had stopped. "I can give you 72. And they're on board your ship, Captain. They have been all along. I suggest you open one up."

Sophia smiled. She had been listening to what was being said in the brig and was relieved that nothing too bad happened. Khan seemed as impossible as usual. And as clever. Kirk would never have believed him if he had told him straight out but this way Kirk wouldn't be able to resist. She bit her lip.

Within a couple of minutes she was back on the bridge. Kirk was explaining what was going on. McCoy seemed unimpressed. "Are you out of your corn-fed mind? You're not actually going to listen to this guy? He killed Pike, he almost killed you, and now you think it's a good idea to pop open a torpedo because he dared you to." Sophia looked down at her padd, trying not to laugh at him.

"Why did he save our lives, Bones?" A very good question.

"The Doctor does have a point, Captain." Spock said. Sophia was surprised to hear him agreeing and apparently Bones was too.

"Don't agree with me, Spock. It makes me very uncomfortable."

"Perhaps you, too, should learn to govern your emotions, Doctor." It that had come from anyone else Sophia would have thought that there was emotion behind it. "In this situation, logic dictates…" Spock continued.

"Logic? Oh, my God! There's a maniac trying to make us blow up our own damn ship and…"

"That's not it." Kirk interrupted. He was smarter than he seemed. "I don't know why he surrendered, but that's not it. Look, we're gonna open a torpedo. The question is how." I frowned, he couldn't really think this was a good idea. Even Kirk wasn't that much of a daredevil.

"But, Jim, without Mr Scot on board, who exactly is qualified to just pop open a four-ton stick of dynamite?" Again, Bones had a point.

"The Admiral's daughter appeared to have interest in the torpedoes and she is a weapons specialist." Sophia wondered if anyone else had worked out who she was. "Perhaps she could be of some use."

Kirk turned back to Spock. "What Admiral's daughter?" He had no idea.

"Carol Marcus. Your new science officer concealed her identity to board the ship." Spock was as calm as ever but Kirk was perplexed.

"When were you going to tell me that?"

"When it became relevant. As it just did." Sophia could have sworn Spock was trying not to smile.


	14. Chapter 14

Once again she looked around the bridge. No-one was watching her so she used ship security to watch what Kirk was doing. He and Carol were walking to the shuttle bay. Carol seemed rather distracted by the idea of opening one of the torpedoes. When they entered one of the shuttles she lost sight of them and switched to looking over medical records, just for something to do.

Some minutes later Kirk was back on the bridge. "Mr Sulu, have Doctors Marcus and McCoy landed on the planetoid yet?" He asked.

"Yes, sir. They're moving the torpedo into position now."

"Good. Any activity from the Klingons?"

"Not yet." She stopped listening. Chekov called in to let Kirk know that they had found the leak but there was a lot of damage. He sounded overwhelmed to Sophia. She listened as Bones flirted shamelessly with Carol and Sophia continued hiding her grin. Carol sounded very professional. Sulu looked at Kirk who shook his head in disbelief. Bones cried out in surprise and everyone jumped.

"Sir, the torpedo just armed itself." Sulu reported. Sophia crossed her fingers and watched the countdown on the screen.

"Four…three…" Bones counted down.

"Shit." Carol swore loudly and it was deactivated. There was silence.

"Doctor McCoy, you alright?" Kirk asked. "Bones?" He said loud.

"Jim. You're gonna want to see this." Bones replied. Sophia knew that the torpedo had just revealed one of the augments.

Sophia slipped out of the bridge and made her way down to the brig. There were two people manning the stations. She smiled sweetly at the man and noticed Khan's eyes flick to her. "I've been asked to make sure that the prisoner is well." She said, indicating her tricorder. The man nodded and she walked over to Khan. She opened the ring and took out her tricorder. "Could you please come over here?" She asked. Khan walked over to the screen and she pretended to scan him. "What's your plan?" She whispered.

"I suspect that the Admiral will come when he hears I have been taken prisoner. He will not be allowed to survive."  
"Yeah, I was talking about the Enterprise. And what can I do?"

"Nothing at the moment. You should go. They will be here soon and you do not want any questions asked." He murmured. She nodded slightly and closed the ring. Smiling at the man again she left the room, just before Kirk saw her. When she saw them entering the room she hung back.

"Why is there a man in that torpedo?" Kirk asked without any preamble. Khan was sitting again.

"There are men and woman in all those torpedoes, Captain." Khan replied. "I put them there." Kirk and Bones exchanged a glance.

"Who the hell are you?" Kirk asked. Finally, Sophia thought, he's realised the Admiral was lying. When Khan spoke he sounded almost nostalgic.

"A remnant of a time long past. Genetically engineered to be superior so as to lead others to peace in a world at war." Nice sentiment but didn't really work. Sophia wondered what Khan was up to. "But we were condemned as criminals, forced into exile. For centuries we slept, hoping when we awoke things would be different." Khan fixed his gaze on Spock. "But as a result of the destruction of Vulcan, your Starfleet began to aggressively search distant quadrants of space. My ship was found adrift. I alone was revived." That was a lie and Sophia wondered why.

"I looked up 'John Harrison'. Until a year ago, he didn't exist. Another person appeared at the same time. Emily Morrison." Sophia bit her lip. That was the name Marcus had given her for when she was working with Section 31.

"John Harrison was a fiction created the moment I was awoken by your Admiral Marcus to help him advance his cause. A smokescreen to conceal my true identity." Khan didn't mention her. "My name is Khan." He seemed a lot more like the monster Sophia had heard about in the eugenics war when he revealed his true name.

"Why would a Starfleet Admiral ask a 300-year-old frozen man for help?" Kirk was being patronising and Sophia wished he wouldn't be.

"Because I am better."

"At what?"

"Everything." It sounded like a joke answer but Khan was deadly serious. "Alexander Marcus needed to respond to an uncivilised threat in a civilised time and for that he needed a warrior's mind. My mind." Khan began to turn away, still talking. "To design weapons and warships."

"You are suggesting the Admiral violated every regulation he vowed to uphold simply because he wanted to exploit your intellect."

"He wanted to exploit my savagery. Intellect alone is useless in a fight, Mr Spock. You…You can't even break a rule. How could you be expected to break bone?" Sophia shook her head. He wasn't gaining any support by insulting them. "Marcus used me to design weapons. To help him realise his vision of a militarised Starfleet. He sent you to use those weapons. To fire my torpedoes on an unsuspecting planet. And then he purposely crippled your ship in enemy space, leading to one inevitable outcome. The Klingons would come searching for whomever was responsible, and you would have no chance of escape. Marcus would finally have the war he talked about. The war he always wanted."

"No. No. I watched you open fire in a room full of unarmed Starfleet officers. You killed them in cold blood!"

"Marcus took my crew from me." Khan turned away.

"You are a murderer!" Kirk was getting angry.

"He used my friends to control me. I tried to smuggle them to safety by concealing them in the very weapons I had designed, but I was discovered. I had no choice but to escape alone. And when I did, I had every reason to suspect that Marcus had killed every single one of the people I hold most dear." Sophia knew Khan was crying. She remembered how he had acted when he had told her to get out of the building. She knew that he wouldn't have bothered to rescue her if he had believed that his crew was still alive but he felt he had to save someone. "So I responded in kind." Khan turned to Kirk and Spock, showing them he was crying. "My crew is my family, Kirk. Is there anything you would not do for your family?"


	15. Chapter 15

Kirk seemed to believe what he was saying. However, Spock had noticed that he hadn't explained something. "Who is Emily Morrison? She appeared at the same time as you but you have not explained her connection." Kirk tilted his head slightly, indicating he felt Spock had a valid point.

"I do not know." Khan lied.

"You are lying." Spock seemed to be far too good at reading people as far as Sophia was concerned. Khan had no answer.

"I am Emily Morrison." Sophia stepped out from her hiding place without thinking. Both officers turned to her. "My real name is Sophia Young. I came aboard under the alias Aurora Young." Both officers frowned down at her.

"You have been on the bridge." Spock stated.

"Yeah, it wasn't hard. You just have to know who to smile at and who not to make eye contact with." Sophia told them, trying to seem more confident than she was. "Khan is telling the truth apart from the fact that I was also woken. Marcus tortured me to make Khan comply with his wishes. I would probably be dead if it wasn't for Khan."

"How did you get on board?" Kirk asked, baffled.

"The same way Carol Marcus did. Forged transfer papers. Doctor McCoy was as easily tricked as you were, no offense Captain." She smiled slightly. "You don't need to worry about me making trouble. Only my brain was augmented. I have the normal strength of a sixteen, or seventeen, year old." She had noticed the two security officers were reaching for phasers. The two officers were saved from replying by the comm.

"Proximity alert, sir! There's a ship at warp heading right for us."

"Klingons?" Kirk asked.

"At warp? No, Kirk. We both know who it is." Khan was enjoying himself too much.

"I don't think so. It's not coming at us from Kronos." Sophia recognised Sulu's voice.

"Lieutenant, move Khan to med bay. Take Sophia too." Kirk looked at her. "Post eight security officers on them." Kirk was running out of the door before he finished talking. Sophia looked at Khan who nodded slightly.

"Yes, Captain."

Sophia and Khan were escorted to med bay by the security officers. Sophia wondered what they would make of the Vengeance as it was almost certainly what was warping towards them. The Enterprise was positively tiny next to it. It was the sort of ship you didn't want to be in a fight with. Khan was instructed to sit on one of the bio beds but the security officers didn't know what to make of a teenaged girl. Sophia stood beside him, chewing her lip. The comm systems were turned on. "Captain Kirk." Sophia closed her eyes and took calming breathes. It was Marcus. She didn't want to meet him ever again. Khan watched her closely.

There was an audible sigh of what sounded like relief. "Admiral Marcus. I wasn't expecting you. That's a hell of a ship you got there." It was the Vengeance.

"And I wasn't expecting to get word that you'd taken Harrison into custody in violation of your orders." Sophia tensed again at the sound of his voice. Khan took her hand and squeezed it softly. She gave him a tight smile in return.

"Well, we, er…We had to improvise when our warp core unexpectedly malfunctioned." Khan noticed that Kirk had not mentioned Sophia. "But you already knew that, didn't you, sir?"

"I don't take your meaning." Marcus sounded shifty.

"Well, that's why you're here, isn't it? To assist with our repairs?" Kirk sounded like he actually believed what he was saying. "Why else would the head of Starfleet personally come to the edge of the Neutral Zone?"

"Captain they're scanning our ship." Sulu said softly. Kirk's voice changed slightly.

"Is there something I can help you find, sir?"

"Where is your prisoner, Kirk?"

"Per Starfleet regulations, I'm planning on returning…Khan to Earth to stand trial." Kirk paused slightly before he said 'Khan'.

"Well, shit." Marcus was talking slowly to buy thinking time. "You talked to him. This was exactly what I was hoping to spare you from. I took a tactical risk and I woke that bastard up, believing that his superior intelligence could help us protect ourselves from whatever came at us next. But I made a mistake. And now the blood of everybody he's killed is on my hands. So I'm asking you, give him to me so that I can end what I started."

"And what exactly would you like me to do with the rest of his crew, sir? Fire them at the Klingons? End 72 lives? Start a war in the process?"

"He put those people in those torpedoes." Sophia glanced at Khan. He didn't seem to be reacting to anything that was said. "And I simply didn't want to burden you with knowing what was inside of them. You saw what this man can do all by himself. Can you imagine what would happen if we woke up the rest of his crew? What else did he tell you? That he's a peacekeeper? He's playing you, son, don't you see that? Khan and his crew were condemned to death as war criminals. And not it is our duty to carry out that sentence before anybody else dies because of him. Now, I'm going to ask you again! One last time, son. Lower your shields. Tell me where he is."

Khan tensed very slightly as there was a moment of silence and Sophia stepped slightly closer, waiting to see what Kirk would do. "He's in engineering, sir. But I'll have him moved to the transporter room right away."

"I'll take it from here." The transmission ended and Kirk was talking instantly.

"Do not drop those shields, Mr Sulu."

"Aye, Captain." The ship wide transmission turned off as they undoubtedly continued talking on the bridge. Sophia took a deep breath and relaxed but Khan stayed as straight backed as ever. Khan looked at Sophia as they both felt the change from the ship being stationary to being at warp.

"Well, at least we're moving again." Bones started scanning Khan's face. Carol stood next to him, looking worried.  
"If you think you're safe at warp, you're wrong." Khan informed them. Carol turned away and ran out of the door. Bones looked baffled.

"The ship has advanced warp capabilities." Sophia informed him. "This ship is slow in comparison." There was weapons fire and the whole ship shook. Khan gripped Sophia tighter so she didn't fall. The shooting continued and people started to fall but Khan stayed where he was, holding Sophia tightly. They were knocked out of warp and the ship spun. Sophia was surprised at how fast it happened. Alarms blared loudly and Sophia stood slowly on her own. The shooting continued moments later. There were screams and reports of injuries from all decks. With no warning he shooting stopped. Sophia looked at Khan. "Carol." He told her and she nodded slightly, understanding. The red alert continued.

* * *

I'm on holiday so I have quite a lot of time, which means more updates. I've just realised that I've been working on this story for over a month.

Anyway, please review and I hope you enjoy.


	16. Chapter 16

There was nothing happening as far as they could tell. They kept waiting for something to happen. Khan seemed to be thinking about what was going on. She suspected he had worked out what was happening. Kirk entered the med bay. Sophia looked up at him but Khan didn't move. Before walking over, Kirk seemed to appraise them. "Tell me everything you know about that ship." Kirk demanded.

"Dreadnought class. Two times the size, three times the speed. Advanced weaponry. Modified for a minimal crew. Unlike most Federation vessels, it's built solely for combat." Khan answered concisely.

"I will do everything I can to make you answer for what you did." Sophia wondered what was coming next as the two men stared at each other. "But right now I need your help."

"In exchange for what?" Sophia rolled her eyes. There had to be something.

"You said you'd do anything for your crew. I can guarantee their safety."  
"Captain. You can't even guarantee the safety of your own crew."

"Bones, what you doing with that tribble." Sophia was baffled by the sudden change in subject.

"The tribble's dead." Bones informed them. "I'm injecting Khan's platelets into the deceased tissue of a necrotic host. Khan's cells regenerate like nothing I've ever seen, and I want to know why."

"Are you coming with me or not?" Kirk asked threateningly.

"What about Sophia?" Khan asked. Sophia knew he would agree but he wanted to seem in charge. "How do I know she will be safe while I am gone?"

"Don't start." She warned. "Captain Kirk, I suggest that both of us help you. I may not be physically enhanced but my mental capabilities far surpass any normal human."

"You want to do what?" Scotty asked. Sophia walked between Khan and Kirk as they were led along the rather boring corridors of the Enterprise.

"We're coming over there. Sulu's manoeuvring the Enterprise into position as we speak."

"To this ship? How?"

"There's a cargo door, hangar 7, access port 101A. You need to find the manual override to open that airlock."

"Are you crazy? Whoever you are." Scotty seemed to realise that the voice was new.

"A little." Sophia muttered. Khan shot her a look.

"Just listen to him, Scotty. It's gonna be all right." Kirk was trying to sound reassuring.

"It is not gonna be all right. You want me to open an airlock into space, whereupon I will freeze, die and explode!"

"You didn't really need to say die. Also your blood will boil." Sophia said. The two men looked at her and she shrugged. It was true.

Sophia sighed heavily as she slipped down into the tunnel like exit. She rolled her shoulders and stood behind Khan, slightly to the left. "Scotty, how we doing over there?" Kirk asked, his voice slightly muffled by his helmet.

"Captain, I wish I had better news. They've locked out access to the ship's computer. They'll have full weapons in three minutes. That means next time if won't be able to stop them destroying the Enterprise. Stand by."

"Captain, the ships are aligned." Spock's voice came over the comm.

"Copy that. Scotty!"

"I'm in the hangar. Give me a minute." Sophia remembered how long those hangars were. "I'm running. Stand by." She glanced at Khan. "Whoa, whoa, hold on, now, Captain. This door is very wee. I mean, you know, small. It's four square metres, tops. It's gonna be like jumping out of a moving car, off a bridge, into your shot glass."

"It's okay. I've done it before." Khan and Sophia looked at Kirk. "Yeah, it was vertical. We jumped onto a…It was a…It doesn't matter. Scotty…" Kirk gave up explaining and Khan looked at Sophia. Both were wondering what they had got themselves into.

"Did you find the manual override?" Khan asked, giving up on Kirk.

"The manual override, Scotty." Kirk said.

"Not yet, not yet."

"Captain, before you launch, you should be aware there is a considerable debris field between our ships."

"Spock, not now. Scotty, you good?"

"It's not easy! Just give me two seconds, all right, you mad bastard!" Khan crouched down and Sophia and Kirk followed. "Okay, Captain, stand by." Scotty said finally. He kept muttering to himself. "Okay, okay! I'm set to open the door."

"You ready?" Kirk asked.

"Are you?" Khan replied.

"Stop it boys." Sophia said, not looking at them but smiling slightly.

"Spock, pull the trigger." Kirk instructed.

"Yes, Captain. Launching activation sequence on three." Green lines appeared on the helmet visor. "Two." Sophia felt butterflies in her tummy. "One." The doors opened and they were thrown into space.

* * *

I'm going to see Black Veil Brides tonight with my friend for her birthday. I hadn't even heard of them until she invited me. Should be fun.

Please review, tell me if I should carry on writing after where it ended in the film.


	17. Chapter 17

There was silence for a moment. "Sir, Kirk is headed for collision at point 432!" A man said.

"Captain, there is debris directly ahead."

"Copy that." Kirk zoomed away.

"Whoa! Jim, you're way off course!" Bones said. You would have thought a doctor would have a better bedside manner.

"I know, I know! I can see that." Sophia dodged slightly, trying to stay focused on where she was going and not be distracted by the other two idiots who had jumped out of an airlock with her. Sophia turned again, making tiny corrections while the Enterprise crew concentrated on Kirk.

"Use your display compass, Captain." Sulu told him. "You must correct precisely 37.243 degrees."

"Got it." He said back. "I'm working my way back." Sophia saw Khan adjust his course slightly. "Scotty, you're gonna be ready with that door, right?" No answer. "Mr Scott, where are you."

"Captain, he can't seem to hear you." Talk about stating the obvious, Sophia thought. "I'm working on getting his signal back. Stand by."

"Damn it." Kirk muttered.

"Captain, what is it?" Spock sounded concerned.

"My helmet was hit. Uhura, tell me you have Mr Scott back."

"Not yet. I'm still working on a signal. His communicator is working. I don't know why he isn't responding."

"Imminent collision detected!"

"Khan, use evasive action. There is debris directly ahead."

"I see it." Khan sounded calm. Sophia did her best to watch but saw him hit something. He spiralled out of control and she focused on where she was going.

"Mr Sulu, did we lose Khan?"

"I don't know, Commander. I'm having trouble tracking him in all this debris."

"He hit something." Sophia said.

"Was Khan hit?" Kirk asked.

"We are trying to find him now."  
"Captain you need to adjust your target destination to 183 by 473 degrees." Sulu told him.

"Spock, my display's dead. I'm flying blind."

Sophia looked around, trying to spot him. "Captain, without your display compass, hitting your target destination is mathematically impossible."

"Spock, if I get back, we really need to talk about your bedside manner."

"Captain, follow me. I'm to your left, slightly ahead." Sophia cut in.

"I'm here. We need to enter on at a time." Khan said. Sophia watched as both men converged on her position. They pulled ahead slightly and exchanged a look. She couldn't believe that they chose that moment to look at each other.

"Scotty, we're getting close. We need a warm welcome." Kirk said. "Do you copy? Do you copy? Scotty?"

"If you can hear us, Mr Scott, open the door in ten, nine…" Spock began a count down.

"Scotty!" Kirk shouted. Sophia tensed, waiting to crash.

"Eight…seven…"

"Mr Scott, where are you?"

"Six…five…"

"1,800 metres. 1,600 metres.

"Scotty, where are you?"

"Three…"

"Do you copy, Scotty? Please!"

"Two…"

"Mr Scott, open the door!"

"Open the door!"

"Mr Scott, now!" The doors opened just in time and they saw someone flying backwards as they flew towards the opposite end of the hangar. They all yelled in surprise as the doors closed and they hit the floor. Sophia couldn't tell what the other two were doing but she started to roll, trying to slow down before she hit something. She felt herself stop rolling and skidded into Khan barely seemed to notice.

"Welcome aboard." Scotty said.

"It's good to see you, Scotty." Kirk said.

"Who are they?"

"Khan, Sophia, Scotty. Scotty, Khan and Sophia." Sophia and Kirk groaned as they got up while Khan looked around.

"Hello." Scotty said.

"They'll know we're here." Khan stated. "I know the best way to the bridge." Sophia smiled at Scotty as she stood up. He seemed surprised to see someone so young.

Kirk started handing out weapons once they were out of their spacesuits. "It's locked to stun." He said as he handed Khan his. Sophia rolled her eyes as he handed her hers.

"Theirs won't be." Khan stated.

"Try not to get shot." Kirk and Khan seemed to be trying to annoy each other.

"You too." Sophia smiled slightly and followed Khan.

"They're gonna have full power and we're walking?"

"The turbolifts are easily tracked." Khan began.

"We would be trapped. This path runs next to the engine room." Sophia took over.

"They know they won't be able to use their weapons here without destabilising the warp core, which gives us the advantage." Khan continued with Sophia beside him.  
"Where'd you find these two?" Scotty asked.

"It's a long story." Kirk replied.

"Not really." Sophia said over her shoulder. "He was sent to kill Khan and I snuck on board the Enterprise."

"I don't mean to tempt fate here, but where is everybody?" Scotty asked.

"The ship doesn't need a full crew. It's designed so it can be flown by only one person if necessary." Sophia told him.

"One? I…" A man came out of a corridor and attacked Khan. The two other men backed away until two more came out of a room and they started fighting. Sophia slipped past Khan and jabbed one man in the neck before he had time to attack. Another tried to aim a gun at her and she twisted it from his hands and slammed it into his chest. Khan punched him and they finished the last person together. Kirk and Scotty were still fighting as Khan dragged Sophia into another corridor.

"When we get to the bridge they will cross us. You must not get hit by one of the phasers. Surrender if necessary but do not get stunned. I may need you."

"You be careful too. Don't do anything too rash."

The sounds of fighting stopped. Khan pulled Sophia further along the corridors and they listened to Kirk and Scotty look for them. "Where are they?" Scotty asked.

"Shit." Kirk said, looking around.

"This way." Khan said, standing not far behind them and Sophia smiled at their surprise. They started walking. Sophia and Khan both heard the plan.

"The minute we get on the bridge, drop him." Kirk instructed.

"And the girl?"

"Keep a phaser on her and it'll be fine."

"Why stun him? I thought he was helping us. Both of them."

"I'm pretty sure we're helping them." Kirk said. They followed after a moment.

The lights started to come on and the four of them stopped being cautious and ran towards the bridge. The power was coming back online. Khan was the first onto the bridge, followed by Sophia. He wasted no time in shooting the officers on the bridge. Nor did the others. Carol took out the guard next to her. Everyone was down and Kirk was pointing at Marcus. He nodded and Scotty stunned Khan and turned his weapon on Sophia. She froze and slowly dropped his weapon. "Take the phaser, Doctor Marcus. Scotty, make sure he stays down." Carol picked up the phaser and aimed it at Sophia while Scotty moved so he could cover Khan more easily. "Admiral Marcus, you're under arrest."

"You're not actually going to do this, are you?" Marcus said.

"Admiral, get out of the chair." Sophia saw Khan's eye open a little.

"You better stop and think about what you're doing, Kirk. You better think about what you did on Kronos. You made an incursion onto an enemy planet! You killed a Klingon patrol. Even if you got away without a trace, war is coming." Scotty looked at Marcus. "And who is going to lead us? You? If I'm not in charge, our entire way of life is decimated! So you want me off this ship, you better kill me."

"I'm not going to kill you, sir. But I could stun your ass and drag you out of that chair. I'd rather not do that in front of your daughter." Marcus glanced at Carol who wasn't looking at Sophia. "You all right?" Kirk asked her.

"Yes, Captain." She sounded shaken.

Suddenly Khan jumped up and slammed Scotty to the floor. "Jim!" Carol yelled too late. Khan launched himself at Kirk and Sophia ducked. Marcus ran towards one of the consoles while Khan beat Kirk up. He threw him across the room and Carol tried to help him. "Listen! Wait!" She tried to stop Khan going after her father but he shoved her aside and stamped on her leg, breaking it. She screamed as he walked over to Marcus and grabbed his head. Carol looked terrified.

"Khan, stop." Sophia yelled as Marcus cried out in pain as his head was crushed.

"You…You should have let me sleep." Khan hissed.

Carol screamed, Sophia turned away and Kirk looked shocked as Khan crushed the Admiral's head.

* * *

So, Khan has got his own back on Marcus and it's almost got to the end of the film. I don't know if I should stop where the film ends and make a sequel or carry on.

I managed to write this, come back from a sleepover (after the concert which was better than I expected) and have my first driving lesson without crashing.

As usual, please review, tell me what you like or don't like, point out stupid spelling or grammatical mistakes and make any suggestions for chapter names.


	18. Chapter 18

Khan began a transmission and forced Kirk to stand so he was visible. "I'm going to make this very simple for you." Khan said, pressing a phaser into the base of Kirk's skull.

"Captain." Spock did not sound emotionless.

"Your crew for my crew."

"You betrayed us."

"Oh, you are smart, Mr Spock."

"Spock don't…" Khan slammed the phaser into Kirk's back and he collapsed. Most of the Enterprise bridge crew moved took and involuntary step forwards to help their captain.

"Mr Spock, give me my crew."

"And what will you do when you get them?"

"Continue the work we were doing before we were banished."

"Which, as I understand it, involves the mass genocide of any being you find to be less than superior."

"Shall I destroy you, Mr Spock?" Sophia shook her head at Khan, just out of sight of the view screen. "Or will you give me what I want?"

"We have no transporter capabilities."

"Fortunately mine are perfectly functional. Drop your shields."

"If I do so, I have no guarantee that you will not destroy the Enterprise."

"I assure you he will not attack." Sophia said, stepping into view. Khan looked at her. "Our crew is on board you ship. Once we have them you will no longer hold any interest for us. Admiral Marcus is dead. We will leave." She glanced at Khan, trying to persuade him to agree.

"Now, shall we begin?" Khan said. Sophia bit her lip.

Spock did not move for several seconds. "Lower shields." He ordered. The shields lowered.

"A wise choice, Mr Spock." Khan kicked Kirk and Sophia hissed. Kirk coughed in pain and Carol looked terrified as Khan walked passed her. Sophia crouched beside her and looked at her leg. Khan scanned the ship. "I see your 72 torpedoes are still in their tubes. If they are not mine, Commander, I will know it." Khan threatened.

"Vulcans do not lie." Spock said, as though affronted by the insinuation. "The torpedoes are yours." Khan beamed them into hangar 7 and smiled as they appeared.

"Thank you, Mr Spock."

"I have fulfilled your terms. Now fulfil mine." Sophia had a bad feeling.

"Well, Kirk, it seems apt to return you to your crew." Khan sat in the captain's chair. "After all, no ship should go down without her captain." Spock looked at him.

"He's locking phasers on us, sir!"

"No, Khan." Sophia shouted as the three Starfleet officers disappeared from the bridge. Khan began shooting.

An explosion rocked the Vengeance, throwing Khan out of his seat and Sophia into a console. "No!" Khan screamed. Sophia realised that the torpedoes were detonating, taking their crew with them. Sophia leant over the nearest console.

"Power is failing. Auxiliary power failing. Hell, everything's failing." She shouted. "The Enterprise isn't doing any better. It's caught in Earth's gravity well. We are too. This ship is going down." She yelled. "Khan, what do we do?" She looked up at him. She seemed to be at a loss. "We need power to shields. Khan, help me." He started to look at one of the consoles, typing in lines of code. The ship fell just past the Enterprise as they tried to stabilise that ship but there wasn't anything to be done.

"Set destination, Starfleet Headquarters!" Sophia didn't complain. Spock had just killed everyone who she had left.

_Engines compromised, cannot guarantee destination. Confirm order._

"Confirm." Khan said. Sophia looked at Khan. She clung to one of the consoles to stay upright. Khan made his way over to her and pushed her down and curled his body around her, using it as a shield to keep her safe. She held on to him tightly as they plummeted.

Sophia screamed as the ship slammed into the ground. She was flung against one of the walls and lost consciousness. Khan held into another console and grimly waited to die as the ship ploughed through buildings. The ship halted. Khan stood and looked around the bridge. There were piles of debris all over it. He began searching through it. Looking for some sign of Sophia. He heard a quiet moan of pain from the far side of the bridge. Where the view screen had been there was a gaping hole, leading down to the street far below. He made his way over to the noise and found Sophia.

A thick metal pole pierced her abdomen, just below her chest. She looked at him with glazed eyes. "Khan." She murmured.

"Shh, don't speak." He started to inspect the wound and she cried out.

"Khan, stop. You have to run. The Enterprise…"

"I won't leave you." She covered his hand with hers.

"I'm not going to survive this. You need to go. Find a way to escape Earth." She drew a shaky breath. Blood was starting to trickle down the sloping floor. "The Enterprise will be looking for you. They'll find me. If there is anything that can be done to save me they will find it but you have to go." She pressed her hand over the wound and smiled slightly. "Go." He turned away. Sophia closed her eyes and waited to drift into darkness.

* * *

I couldn't resist using the title in the story, it was too tempting

Anyway, what is going to happen to Sophia?

Thank you to everyone who reviewed, I might not be able to upload as often because it is always busy at Christmas time. I intend to upload on Christmas day, maybe before then as well.


	19. Chapter 19

There was the sound of a transporter and someone cursing as they slipped. "Sophia, where are you?" She whimpered slightly and heard footsteps approach. Several people in blue Starfleet uniforms surrounded her. Doctor McCoy crouched next to her, already scanning her. "She's lost a lot of blood. We need to be beamed up. Make sure they don't get that pole. Have a medical team standing by." Sophia closed her eyes and blackness engulfed her.

Sophia woke in a white room. Bones was standing over her. "Good morning. How do you feel?"

"D'you want the truthful answer or the polite one?" She mumbled.

"That good. Well, you're almost better. Khan's blood works wonders." He was scanning her. "Is there any pain?"

"Yeah, but I think that I just ache all over from lying down for too long. What happened? I remember seeing you and then I'm not sure what happened."

"Well, you almost died of blood loss and I saved your life. We would have got you out earlier but we were dealing with Kirk." Bones leaned over and tapped a few buttons on the panel over her head. He saw her raise an eyebrow. "He died of radiation poisoning and was saved by Khan's blood."

"How is he?"

"He's still in a coma. Hopefully it won't be for much longer." Sophia nodded and closed her eyes for several seconds.

"What's going to happen to us?"

"You mean the augments and you? Khan's already in cryogenic suspension and the rest of the augments are with him."

"But…" Sophia began.

"No, Spock had them taken out of the torpedoes. They're safe. You, we don't know what's going to happen. There have been some debates. I think they're waiting for Kirk to wake up so he can tell them what he thinks. No-one really knows what to make of you. You haven't actually done anything wrong but some have argued that you were supporting Khan, therefore aiding a criminal."

"I also forged documents to get onto the Enterprise." She smiled slightly. "It was surprisingly easy."

"Well, you helped us get on board the Vengeance. That's got to be in your favour." The doctor looked down at her. "What do you want to happen?"

"I don't know. The only people I really know are all frozen. I don't want to leave them undefended. A lot of people will want revenge. I also don't want to be the only one unfrozen because I could end up dead long before any of them are woken up."

"You could make new friends." He suggested.

"I don't think so. I'm half augmented. No-one will want to make friends with me."

Sophia spent the next few days in bed. Doctor's orders. She slept most of the time. Bones woke her one day with the news that Kirk was awake. She insisted on talking to him. She knocked on the door softly. "Come in." She opened the door and entered the room.

"Hello, Captain." She said softly.

"Sophia, you survived." She smiled. "Why are you here?"

"Bones won't let me go. Not that I have anywhere to go." She frowned. "Captain,"

"Call me Jim." Kirk interrupted.

"Jim, I am probably going to be in a lot of trouble for being what I am. I need to know what you are going to say if you are called to testify at my trial."

"Is there a date for your trial?"

"Yes. Bones doesn't know that I know. They've set it for two weeks. They think you'll be well enough by then."

Kirk looked at her. She seemed very young to be fighting the whole world. "I think that I will be telling them that you did your best to stop Khan from killing us. You came aboard my ship to help Khan, but not to kill anyone, to stop him doing something…" Kirk searched for the right word.

"Rash?" She suggested.

"That's as good a word as any. Don't worry. I don't think you're a murderer."

"Thank you, Jim." She relaxed slightly.

"So, how did you get caught up with Khan and his lot?" Jim asked. Sophia laughed and sat down in the chair next to him.

"I am one of them." She told him.

"Well, sort of. Come on. Tell me how you ended up 300 years out of time on a spaceship with a bunch of augments. I am so unbelievably bored of staring at the ceiling." He smiled and she started to explain what happened.

Sophia looked at the dress she had been given to wear. It was too short. She glared at it and sat down. In two hours she was expected to be at her trial and she had no intention of wearing a dress that short. There was a knock on the door. "Come in." Carol entered the room.

"You aren't dressed." She said.

"No, I'm not wearing that dress." Carol looked at it and tried to supress a laugh.

"Good thing I brought this." Carol produced a bag and handed it to her. She looked inside and found a set of clothes, including trousers. She grinned as Carol sat down and went into the bathroom to change. Sophia came out wearing the top and trousers. They were black and contrasted shockingly with her pale skin and blonde hair. "Shall we?" Carol asked.

"I think it might be wise. I wouldn't want to be late for my own trial after all." She smiled.

As soon as Sophia opened the door two security guards turned to look at her. She and Carol exchanged a look of slight amusement. Carol thought it Sophia was amused because she was only a teenaged girl and they thought that she was a danger. Sophia was amused because she knew she would be able to take out both guards very easily. Carol led her to the court room. There were a lot of people in it.

* * *

Next update will probably be on Christmas day.

Please review and any suggestions for chapter names are much appreciated because I intend to give all the chapters proper names at the end.


	20. Chapter 20

Sophia sat next to Kirk and Carol. They had insisted on supporting her in the trial. The first few hours were very boring. Lots of people spoke but they said very little. Eventually Sophia was called to talk. She stood took several calming breathes. "Would explain to the court how you ended up in this time." The judge asked.

"In my time the augments were being overthrown. I knew that normal humans would come for me very soon so I boarded the SS Botany Bay and put myself into cryogenic suspension with Khan and his crew." She said calmly.

"Please explain why you felt the people of your time would feel it necessary to attack you."

"My mind has been augmented." There were some mutters. "Although I have the normal strength of a seventeen year old human I have far greater mental capacities."

"Why were you helping Khan?"

"Because it was the right thing to do." There were angry whispers at her statement. "Forgive me, but in this time I was tortured, threatened and forced to watch as twelve defenceless people were murdered in front of me. As far as I could see, Starfleet was the enemy." Sophia wondered if she was saying the correct things.

"Please tell the court exactly what happened from the time you woke up." The judge said.

Sophia looked at the people around her. "I was woken in the headquarters of Section 31, a clandestine section of Starfleet. The headquarters were under the Kelvin memorial building, the one Khan attacked. As soon as I was well enough I was put into a cell with the augments. They were not particularly pleased to have me there. Every day I was taken out of the cell and interrogated by Admiral Marcus and his people. After several days Khan decided to put me under his protection. When he refused to let me go to be interrogated Admiral Marcus had us attacked. We were overpowered and all except Khan and I were put back into stasis. Marcus told Khan that if he didn't work for him I and the other augments would be killed. I was kept awake to ensure Khan's cooperation.

Sophia took a breath and continued. "For the next month or so I was kept locked up. In that time Khan came up with a plan to save his people. Marcus found out about it and took us both to where he was keeping the cryo-tubes. He said that he was going to kill half the crew. I convinced not to. Instead he killed twelve of them and tortured me for several days." Sophia hurried on. "A couple of months later I also started working for Marcus. About a year after we were woken, Khan disappeared. Marcus thought I knew something so he left me in a cell for several days with no food or water. He found that I didn't know anything and I woke up in a med-bay some days later. Khan helped me escape and I stayed in a flat he had rented. Two days later he was involved in the destruction of 31. I boarded the Enterprise as a nurse and followed Khan.

"When Captain Kirk was talking to Khan I revealed myself because they knew that a girl named Emily Morrison had appeared at about the same time as John Harrison. I was given the alias Emily Morrison by the Admiral. I was on the boarding party to the Vengeance. I tried to stop Khan firing on the Enterprise." Sophia finished and looked around the room. There were a lot of murmurs.

"Did you try to stop Khan crashing his ship into San Francisco?" The judge asked.

"Khan tried to crash into Starfleet headquarters, he wasn't interested in harming the civilian population. But no, I did not try to stop him. We both believed that the only other people we knew had been killed by Commander Spock. I wanted revenge although I would have preferred it not to be on such as large scale however I knew that no-one would be able to stop Khan. He would do anything for his crew and to believe them dead after trying so hard to save them was devastating to him."

"Do you think that Khan was right to try to attack Starfleet?"

"No, but I do understand his actions. If Spock had not tricked Khan into believing his crew were dead those people would not have died but I understand why Spock did what he did." The judge continued to question Sophia for almost half an hour. Finally she was allowed to sit back down.

Jim was asked to speak next. "I believe that Sophia Young is able to justify her actions. From the time she was woken up she was in constant danger and tortured at least once. She followed the one person who had been nice to her in this time. Although she did board the Enterprise illegally she was not trying to endanger the crew or the mission or damage the ship. She did her best to stop many deaths and helped us board the Vengeance. I think that all charges should be dropped and that she should be looked after. She's only a kid and she's been tortured by one of our most respected people." Silence met his statement. Sophia wasn't sure if it was a good thing or not.

The trial continued slowly for the next few hours. Sophia was getting more and more nervous as the jury talked. They seemed to be arguing over something. She tried to breathe calmly but she could feel adrenaline racing around her body, making her hands tremble. Jim smiled at her, trying to be reassuring. "Jim, have they decided what's happening in Khan and his crew yet?" She asked quietly.

"Not really." He whispered back. "They've said that they'll all be kept in cryo until a better solution is thought of. No-one really wants to make a choice so they're just going to let them sit in storage somewhere until someone else comes along and steals them." Sophia nodded, mind whirring.

"The jury have made a decision. Would Miss Young please stand." The judge said. Slowly Sophia stood and walked down the steps. "The jury have decided that Miss Young should be cleared of all charges." Sophia smiled slightly and relaxed. "However, it has been brought to our attention that she is under the age of 18 and is in need of a guardian." There were a few mutters. "There have been several offers to look after her but it is necessary that we have an official guardian."

"I'll be her guardian." Sophia turned around, surprised to hear Bones' voice. "It's not like I have anywhere else to be until the Enterprise is ready."

* * *

Merry Christmas everyone.


	21. Chapter 21

Bones looked down at his new charge. She smiled impishly up at him and he resisted the urge to groan. What had he been thinking? Taking on a half augmented teenager was sure to end in trouble. "Alright then."

"D'you have any children?" She asked. Bones sighed. It was going to be a long day.

"I have a daughter. She lives with her mother. I live alone. Or I did." He frowned. "I probably ought to show you where you're going to have to stay for the next however many months."

"About ten months until I'm 18, I think. That would be 18 years not in cryo." She clarified.

"I guess we'll have to work out when you do actually turn 18, for legal stuff." He frowned again.

"This is my place." Bones turned on the lights and Sophia looked around the room. It was a small hallway. She could see several rooms through the open doors. There was a living room, a kitchen and a bedroom. "You'll be staying in here." He pushed open one of the doors. It didn't take long to show her around the flat. He glanced at his watch. "It's getting late. Do you want to go out or I can make something here?" Bones knew he couldn't actually cook to save his life but he felt he ought to give her a choice.

"You don't cook often." She said, looking at one of the padds.

"How do you know that? Has Jim been talking about me?"

She grinned at him. "There's dust on all your pans."

"Alright, I can't cook."  
"I can. Do you like drop scones?" She put the padd down and started towards the kitchen.

"Why would you drop a scone?" Sophia rolled her eyes and started pulling out ingredients.

Sophia spent the next few months learning. As far as Bones could tell, she did very little other than read and swim. Most days she would go to the nearby swimming pool for a couple of hours. Sophia felt bad about going behind Bones' back but she knew he wouldn't agree to what she was planning. As well as learning everything she could about the century she had woken in, she was learning about star ship operations and which planets were m-class and not in Federation space, but not too far away either. At some point she knew she'd have to hack the Starfleet database to find out where Khan and his crew were being kept but she was putting it off. She was also looking for a ship which would be big enough for 74 people and had large cargo bays. Bones was completely oblivious to what she was up to.

As Sophia got closer to turning 18, Bones was being given more assignments further from San Francisco. It was useful for her because she was starting to collect a lot of things they would need to form a colony. She knew that she'd need money before long and somewhere to store all the things she would need to buy. A couple of times she had looked at the security around the Starfleet databases. It was thorough. But given time she was confident that she would be able to find Khan and his crew. After a couple of months she realised the enormity of the task she was trying to undertake.

She decided the first problem to counter was money. She would need money to buy a ship and all the equipment. When she had decided what she was going to try to solve it was easy to solve it. For a couple of weeks when Bones was away she dressed in heels, put she hair up and some make-up on and went gambling. She cheated in every way she could. Counting cards and using maths to work out the possibilities of something happening meant she could win far more often than was strictly fair. She never stayed in one place too long, or won so often it was obvious she was cheating. Over the weeks she gained several types of currency, not knowing where they might end up. Sophia had found several possible planets to colonise but she wanted to look at what the Starfleet database said about each one first.

Over the days which followed started to store everything in a large warehouse which no-one else had any interest in. The biggest problem was finding a ship. Very few people would sell a large warp-capable ship to a teenager. Sophia had started to look at ships which were about to be sold to scrap yards. She guessed that she would be able to fix one up well enough to use it to get them out of Federation space. There were several she reckoned would be alright. One of them wasn't far from San Francisco.

Sophia looked at herself in the mirror critically. She was going to see the best ship she'd been able to find. It wasn't perfect but it was big, not too damaged and old enough no-one else wanted it. She had forged an I.D. and had most of her money. Her hair was pulled back into a high bunch and she was wearing just enough make-up to look a few years older. She wore trousers and a t-shirt with long brown boots which were comfortable and easy to run in, just in case.

Sophia dumped her coat on her bed and sighed heavily. The ship was old and in need of repair but she knew she'd be able to sort it with time. She had bought it and some spare parts. The man had sold it to her incredibly cheaply for what it was but she supposed that he didn't believe she would be able to get it running again so it wasn't worth much. It was hidden in the warehouse with all the other things she had gathered. Although it wasn't much to look at she was quite pleased with the ship. She started working on it that day.

Weeks rushed by until the ship was finally ready to go. She had been staying with Bones for six months. When she wasn't working on it, she was getting supplies. She had made a list of everything she could think of which they might need and it kept growing. Bones had noticed that she seemed very busy but she claimed that she was doing a project, and in a way she was. She had found that the money she'd accumulated was running out and had had to go out several times to get more. It was getting to the point that she couldn't just ignore the problem of not knowing where the cryo-tubes were. The ship was working very well, she had almost everything on the list but she needed the cryo-tubes.

* * *

Sorry for the delay. We had family over and were busy so I didn't have much time to write. I've also got homework to do and lots of books to read :). Please review, make comments, suggest chapter names, suggest what could happen next etc.


	22. Chapter 22

One day Bones went out, telling her that he would be out late. Sophia instantly started to get ready. She picked up the padd which she had fiddled with until it was completely untraceable. After grabbing a coat and shoes she slipped out of the door, locking it behind her. Sophia went to as small café and accessed the public information from Starfleet. From there she started to look at the less freely available information. She quite enjoyed the challenge of getting into their system. It stretched her mentally, which was unusual, and required all her thoughts so she couldn't wonder about the possible consequences of hacking in Starfleet's most secure databases. After several hours digging she found them. They were being stored in an underground base in Alaska. They would be moved in under a week, off planet. It didn't say where.

Sophia paid for her drink and left quickly. She wanted to run to the warehouse but she needed to think. There were still things she needed to buy and the ship needed to be loaded, or as loaded as it could be before she put the cryo-tubes in the cargo hold. As soon as Sophia got to the warehouse she checked what she had. She went into the ship and looked around, deciding where to store what. There were forty rooms for a crew, a med-bay, a kitchen, a dining room, an engineering section, a couple of large rooms for whatever they might be needed for and two large cargo bays.

She started to pack the stuff in. It wasn't until she almost broke a toe by dropping a welding torch on it that she gave up for the night. Bones wasn't back when she got back to the flat so she fell into bed fully clothed. The next two days were almost the same. Sophia would get up early, leave a note for Bones with an excuse and continue packing the ship. The day after, she discovered that the fates were in a good mood, Bones was going away for a couple of days.

Sophia looked around the flat one last time. She couldn't help wondering if she would ever see Bones again. Somehow she doubted it. Swinging her backpack onto one shoulder she closed the door, locked it and left without looking back. She walked to the warehouse, hoping she was doing the right thing. The ship seemed far smaller when it was packed with everything she could imagine they might need. On the bridge she sat in the captain's chair and tapped the screen set into its arm. The panel lit up and soon the engines started to hum. "Come on then." She muttered. "Let's see what you can do, Dawn." She had named the ship 'New Dawn' since the augments were having a new start, it seemed appropriate.

As carefully as she could, Sophia set the ship down in the middle of a snowy field. She was high in the mountains of Alaska and it was freezing. Sophia leant over one of the consoles, scanning the area carefully. For almost five minutes nothing happened. Then there was a beeping. Her fingers flew over the panel as she checked the results. She flipped on the engines, knowing she might need to make a fast get away if anything went wrong. She sat back in the captain's chair and started to hack into the security cameras. She put them into a loop. No-one would notice that it was the same image over and over again because nothing about it changed.

The transporter locked onto the first lot of cryo-tubes. Sophia watched as they appeared in the cargo bay. She grinned and locked onto the next lot. As soon as all the tubes were on board she set a path out of the Sol system and towards Ceti Alpha V. It seemed to be the best of the worlds to settle on. As soon as they were out of the solar system, Sophia pushed the ship into warp, praying it wouldn't fall apart. She left it on automatic and half ran down to the cargo bay holding the cryo-tubes. They were all bunched up next to each other but she soon found Khan's. He was smiling slightly in his sleep. For a moment her hand hovered over the controls to wake him. But she turned away. It wouldn't be good for Khan to believe he could get back at Starfleet for what they did to him, particularly as their ship was ancient and almost completely unarmed.

That night, Sophia set the computer to alert her if anything happened and lay back on the mattress she had moved to the ready room, just in case something happened. She smiled as she thought about the cryo-tubes sitting safely in the cargo bay. They would be safe within days and no-one would know where they were, hopefully.

On Earth, Bones arrived back at his flat early. He looked around for Sophia but didn't find her. Her room was completely empty of her things. There was only a padd sitting on the pillow of her bed. It read:

Dear Bones,

I'm sorry for doing this but my conscience wouldn't allow anything else and I couldn't let anyone know. I probably won't ever see you again because I've made the decision. The augments should be allowed to live in peace. Khan did some bad things but the others haven't done anything wrong and Khan never hurt me so I can't just leave him. The augments and I will colonise an m-class world outside Federation space and hopefully be left in peace.

Thank you for looking after me. You didn't need to and I am grateful for it. I know that I have no right to ask this of you, but please, don't tell anyone what I've done, at least for a little while. The augments won't be a threat. They are all together and as long as no-one tries to change that they will not want to hurt anyone else.

I'm sorry,

Sophia Young.

Bones stared at the padd for several seconds. She was gone. Looking back, he realised that this had been her project, the reason she spent all her time working, the reason she was so guarded most of the time. She could never have been happy not knowing what would happen to seventy-three people whom she viewed as innocent, or mostly innocent. He dropped the padd back on the bed and pulled out his communicator. Then paused. Why not let them get away? It would certainly solve a lot more problems than it would create and no-one needed to know that he had read what was on the padd earlier than Sophia would have expected. Bones left the flat, locking it behind him, and walked towards San Francisco bay. Sophia had liked it there and he felt rather sentimental.

Sophia woke up because she had rolled off the mattress. She got up and went onto the bridge. Nothing interesting had happened so she went to have a shower and get changed. She didn't know how long she would have before something went wrong and she intended to make the most of her time before then. After showering and changing she went to the kitchen and found herself some food.

The days on the ship blurred into one as she kept an eye on all the systems and fixed the few which broke. Nothing too bad happened and Sophia was getting nervous as they got closer to Ceti Alpha V. Bones would have found her note and know what she had done. Starfleet would know too and she would almost certainly be considered a criminal. With that in mind she kept the ship at high warp.

* * *

Sorry it took a while. We've been really busy.


	23. Chapter 23

The computer beeping woke her. Sophia sat up and rubbed her eyes. The computer beeped again and she got up and looked at the panel. It told her the ship would drop out of warp in five minutes because they had almost reached Ceti Alpha V. Sophia grinned. They were so close to being safe. She ran off the bridge and changed into new clothes as fast as possible, then ran back. She was back before she ship came out of warp. It didn't take her long to confirm that there were no signs of intelligent life on the planet. She left the scanners on to find the best place to land and went down to med-bay. Khan's cryo-tube was lying on the floor next to one of the beds.

Sophia looked at Khan's face. He was smiling slightly. She wondered why as she typed in the activation sequence. The tube opened and she lifted Khan out with some difficulty. She laid him on the bed and ran a scanner over him. He was waking up fairly quickly. She guessed that it would be easier to be in cryo for only a few months rather than over 200 years. She watched as the device tracked Khan's increase in heart beat and respiration rate. She couldn't see anything wrong and the device didn't start beeping in protest so she guessed everything was alright. Slowly Khan opened his eyes. Sophia smiled and threw her arms around him. He looked around slowly after hugging her for a moment. "How do you feel?" She asked, letting go of him.

"Where are we?" He ignored her question.

"In orbit of Ceti Alpha V. Now, tell me how you feel. I need to know if anything has gone wrong." Khan seemed to be thinking about his answer.

"I feel tired. But that is to be expected. Why did you bring me out of stasis?"

"So your crew…" She was cut off by Khan's hand closing around her throat. Her fingers scrabbled at his.

"My crew is dead." He hissed, bring in his face close to hers.

"No." She choked out. He let her drop and she gasped for air, hand massaging her throat. "They aren't dead." She gasped. "Spock took them out of the torpedoes. They're in the cargo bay." Khan looked down at her. She stood up, hand still resting on her throat. "They are all down there."

Khan didn't speak for almost a minute. "You saved them."

"Starfleet were just going to leave you in storage somewhere and hope that the problem would go away. I couldn't leave you there."

"It seems I owe you an apology."

"No, you couldn't have known." She smiled slightly. "Come on. I'll show you." Sophia showed him down to the cargo bay. Khan stood in the doorway for several seconds, not quite able to process that his crew, his family was still alive. He moved among them, looking down at each face. Soon he turned to Sophia who was standing in the doorway.

"Why are we in orbit of this planet?"

"It seemed the best one to form a colony on. No-one else lives here. M-class. Reasonable weather and not too many earthquakes. Not in claimed space. It seemed the safest place to come. We can start again with no-one chasing us. No-one knows where we are."

"Are you sure?"

"Yes. They'll know that you've disappeared by now and that I'm gone but apart from that, we are safe. No-one knows I've got this ship and it works. I don't want to be caught considering I probably broke a dozen laws freeing you, not to mention forging documents, waking you up as well."

"You have thought about this a lot." Sophia fixed him with an irritated look.

"I planned everything about it. I've collected everything I can think that we might need, for 74 people. I bought a ship, illegally I might add, and I got you out of a secret Starfleet base."

Khan looked down at the girl with increased respect. "Why?"

"I couldn't just leave you there." She sounded outraged at the idea. "Anyway, you're the closest thing I had to a family for a long time."

Although Khan had a feeling that she wasn't telling him something he let it go. They were safe and that was all that mattered. "Have you found somewhere for us to settle?"

Sophia smiled. "I found a planet but not the specific place. There is rather a lot of planet to scan. The computer only started just before I woke you up. You are still feeling alright aren't you?" She checked. Khan raised an eyebrow and she smiled at him. "Do you want to wake the others up now or wait until we find somewhere to put the ship down? There is enough room for everyone on the ship but it's a little cramped."

"You really are unbelievable." He said. "You did all this by yourself."

"I had to. Anyway, you saved me plenty of times. Now, where do you want to wake them up?" She crossed her arms and waited for him to give her an answer.

"On the planet I think. They should wake up in their new home."

Sophia next insisted on leading Khan to the kitchen so they could both have something to eat. She had explained that it would take several more hours for the computer to gather all the data and there was no point sitting on the bridge waiting. As they walked through the corridors Khan became more impressed with Sophia. Several side corridors were almost completely blocked off with things they would need. "Alright, what do you want? I can make stir fry again, that's quick. Or something else."

"Whatever you want to make." Khan was looking around.

"Khan, if you want to look around I can call you on the comm system when the food is ready."

Once they had eaten Sophia showed Khan around the ship, particularly engineering and the bridge. She had had to improvise with some of the engineering and Khan was surprised that it all worked so efficiently. He wasn't so impressed by her way of kicking one of the consoles on the bridge to make it work but, as she explained, it was the best was of making it work without looking at every wire to try to find the lose one. After she had explained everything she took him into the ready room. Khan raised an eyebrow at the mattress on the floor. "Why have you been sleeping in here?"

"Oh, yeah, well I was the only one on the ship who was awake so I wanted to be near the bridge or engineering if something went wrong and the bridge has an engineering station so it seemed better to stay up here."

"Naturally." Khan didn't seem to agree but he wasn't going to argue either. "Now, shall we look at what the computer has found for us?" Sophia rolled her eyes but followed him back onto the bridge.

* * *

Thank you to everyone who has reviewed. School starts again tomorrow so I might not be able to update for a few days, sorry if that is the case.

Reviews make my day. *Hint hint*.


	24. Chapter 24

They spent the next couple of hours coming up with possible locations to settle in. There were several options which looked promising but they weren't certain which was best. One was fairly far to the north, and as they didn't know how bad the winters would be they weren't sure it was a good idea to risk it. Another was more likely to have a temperate climate but the soil was very acidic. Their final option was a valley in a mountain range. They would be fine as long as there wasn't any bad weather, at which point they would be stuck.

They decided that the mountain valley would be the best one to choose. There was plenty of space and it wasn't too high. It also wasn't too far from the sea so the climate wasn't likely to change as much. Sophia led the way to the bridge and sat in the pilot's chair. Khan raised his eyebrow. "Why not the captain's chair?" He asked.

Sophia turned to him. "I thought that you would want to be in charge."

"It's your ship."

"Which is why I'm the one controlling it rather than sitting in a chair looking pretty."

"Is that what you expect me to do?" She flashed him a smile and turned back to the console.

They landed without a problem and went down to med-bay. "Who are we going to wake up first?" Sophia asked. In their spare time they had moved half a dozen tubes up to med-bay.

"We wake Kati first." He strode over to one of the tubes. Sophia grabbed a tricorder and punched in the activation sequence. When it opened, Khan lifted the woman onto the nearest bed. She had short black hair and looked fairly small of stature. Khan watched the information on the screen of the tricorder as Sophia ran it over the woman. She was waking up more slowly than Khan had but she had been asleep longer so it was expected. When she opened her eyes they settled on Sophia and Khan. "Khan, what happened?" She started to sit up but Sophia put a hand on her shoulder to stop her.

"I need to do some scans before you get up."

Kati looked like she would disobey until Khan spoke. "Do as she says. We would not be here if it were not for her." Khan started to explain what had happened as Sophia checked Kati's health.

Sophia put the tricorder down. "As far as I can tell, you're fine." She said. "I don't suppose that you have a doctor who would be able to do this?"

"We do have a doctor." Sophia looked at Khan, entirely unimpressed.

"Then why didn't you wake him up first. He's far more likely to know if there is something wrong with you."

Kati looked at Khan. "She does remember we're augments, right?" Sophia shot her a look which said something along the lines of 'go die in a hole'. Khan smiled slightly and started to look over the other cryo-tubes. Kati turned to Sophia. "You've changed. And he's changed." She jerked her head at Khan. "What isn't he telling me?"

"Ask him yourself." Sophia turned away but Kati caught her arm.

"Thank you." She said. "For helping us, and him. He hasn't been the same since our sister died."

"You're siblings." Sophia looked shocked. Kati laughed and nodded.

"Khan probably didn't tell you in case Marcus found out. He's not good at talking about family. It's stupid really."

"Kati, if you want to survive the next five minutes I suggest you shut up." Khan's voice came from the other side of med-bay. Sophia sniggered as Kati replied.

"I hope you're not suggesting you could beat me at something. I might feel inclined to embarrass you if you were. Or I could just beat you up." She smiled.

Khan came back into sight. He threw a glance at Kati which said a lot and then addressed Sophia. "Do you want to wake Otto next? He is the closest we have to a doctor." He added at her perplexed look.

"Yeah, that would be helpful." Sophia smiled slightly. "Is his tube up here or do we have to bring it up?"

"It is here." Khan led her over to one of the tubes. Sophia raised an eyebrow.

"How old is he? I mean, he doesn't look much older than I am."

"He isn't." Khan leant over and punched in the activation sequence. Sophia didn't bother trying to work out how a teenager was the most qualified doctor among them. Khan lifted Otto onto the bed next to him and Sophia ran the tricorder over him. She watched the readings change slowly until he opened his eyes. Both Khan and Kati were standing on the other side of the bed. He blinked several times, looking around. "Hello Otto." Khan almost sounded gentle.

"Khan, what's going on?" He looked around suspiciously. "We aren't in that building anymore."

"No, we aren't. We are on another world." Khan explained. "We are going to colonise this world." Kati looked at him in surprise.

"You left that part out." She said. "What happened on Earth?"  
"We crashed a ship into San Francisco by accident. Khan was aiming for Starfleet because he thought Spock killed you all." Sophia explained. All three looked at her but she was already concentrating on the tricorder again. "Alright, I think you're alright but you might want to check considering you're a doctor and I'm not." She shot a look at Khan as she handed the tricorder over.

"I don't know how to use this." He pointed out. Sophia sighed softly and started to explain.

Khan watched with approval. He was pleased that at least some of his crew seemed to be accepting her without complaint. She explained how to use the tricorder with patience. It only took a couple of minutes for Otto to catch on. He did a couple of practice scans before Khan woke the next person. Sophia watched carefully, occasionally explaining something to him, like how to work a hypospray. There wasn't much for her to do but she stayed anyway. Khan spent most of his time answering his crew's questions. Sophia sat on one of the free beds, leaning against the wall. She couldn't help smiling as she saw Khan's very slight smile. He was happier than he had ever been around her.

Sophia found herself almost falling asleep. She wasn't sure how long it was since Kati was woken but it had been a long time. She'd stayed with Khan and Otto while they had woken the sleeping augments and it had taken a long time. There were still a few more to wake before Khan would have his family back and complete, or as complete as it could be after Marcus had killed some of them. She rubbed her eyes and tried to concentrate. "Sophia, go to bed." Khan stood next to her. She hadn't noticed him come over. "You've been awake for hours. Go and sleep. Nothing new is going to happen until everyone has slept for a while." Sophia considered protesting but knew that she would just end up falling asleep in med-bay if she didn't sleep soon. "Now." Khan said. She slipped off the bed and started towards the door. "Sophia." She turned back to him. "Don't go up to the bridge." She rolled her eyes.

Khan looked down at Sophia. She had fallen asleep fully clothed. It had been hours since he had sent her to sleep and he knew that she would want to know what was happening. Everyone had had a couple of hours sleep at the very least and Khan wanted to have a meeting and explain what had happened to everyone but he knew that Sophia would want to be there. However, he also knew that she needed more sleep than the rest of them did. Deciding that she would probably need to know what was said he shook her shoulder. She opened one eye for about a second then closed it again and groaned. "You don't sleep enough." She grumbled.

"We're going to have a meeting. Everyone together. I thought that you would want to know because they will almost certainly have questions for you by now." She sighed but got out of bed anyway.

"Where's the meeting going to be?" She asked, looking around the room, only half awake.

"In the dining room. Ten minutes." He told her and left the room.

Sophia slipped into the dining room and looked around. Most of the people were already in there. She sat in the back and tried not to draw attention to herself. Several people looked her way but none said anything to her. A few minutes later Khan entered the room. Everyone fell silent instantly and Sophia was reminded of a teacher entering a classroom. She didn't really listen to his explanation of what happened after the others had been put back into cryo. She knew the story. She only half listened to the questions which followed. Finally the questions turned to what would happen next. She began to listen to what was being said at that point. "We are going to settle on this planet. It is away from the Federation and no-one else knows where we are. We will be safe to do as we please away from danger." Murmuring broke out among them and Sophia smiled. Most of them seemed pleased with the new development.


	25. Chapter 25

For a couple of days the augments rested, recovering from their time in stasis. Sophia spent the time making friends and cooking because very few of them could cook anything properly. She didn't mind cooking really, although she intended to teach at least some of them. There were a couple who she avoided as much as she could. They weren't very happy about having her there. She barely saw Khan in those days. Kati, Suzette Ling and Otto became her closest friends. Otto was not the only one around Sophia's age but she was the only one who wanted to talk to her. Most of them seemed to feel that she was unimportant.

Once they were completely recovered they started to work. The area they had chosen was on the edge of a forest and it didn't take long for the first trees to fall. They made small log houses which would be added to in time. In only a couple of weeks they were finished. Sophia had been amazed at how fast the augments worked. In the eugenics war she had seen them fight but she had never seen them build. It took six people approximately two days to complete a house. Sophia found out early on that it was more helpful if she stuck to the theoretical side of building and made sure that there was plenty of clean water to drink. Otto was kept busy with injuries from construction and complained that they should be more careful. Sophia wasn't sure if she was surprised or not about Khan helping with the work. In the end she decided that it wasn't really that much of a surprise. He wanted to help his people and would in any way he could.

The months which followed were hectic but happy. Sophia was accepted by most of Khan's people. She taught a lot of them how to cook and use the new technology. Several gardens sprung up which all of them helped look after. More than a few couples formed and several people moved in together. Sophia was particularly excited when Joaquin and Suzette moved in together. There was even talk of a wedding. It would only be a matter of time before there were children.

One warm day Kati asked, or insisted depending on your point of view, that they try to climb the mountain nearest them. 'They' were Khan, Sophia, Otto, Suzette, Joaquin, Alcester, who she insisted was not her boyfriend, and Kati herself. They packed bags with what they would need for a couple of days walking and camping and left, leaving Rodriguez in charge. Sophia didn't like Rodriguez. She wasn't sure why but they could never get along, so they avoided each other as far as possible without being rude. The others had insisted on taking most of Sophia's stuff for her. She had complained but Otto had refused to take no for an answer and pointed out that she wasn't as strong as them. She had insisted on carrying some of her things but she had suspicions that it would get lighter if she left it alone for more than a few seconds. Just before they were due to leave Kati announced that they had another person joining them. That person was Jade. Sophia was amused. It was plain that Kati was still trying to set Khan up with someone. So far she had failed rather spectacularly.

It was about an hour after the sun had risen when the set off. It was a comfortable walking temperature but they knew that it would get hot quickly. With this in mind, Sophia had plaited her hair tightly and pulled it half way through a hair bunch so it hung in a loop off the back of her neck. They walked for several hours before stopping. Sophia suspected that it was for her benefit more than anyone else's. Kati almost dragged Khan over to Jade and then left them. Sophia dumped her bag at the bottom of one of the trees and started to climb. She stopped on a thick branch and looked around happily. She could back down the slope to the village. There were tiny people moving about among the houses. After a few seconds she heard Otto climbing the tree. It took him far less time than it had taken her. She moved along the branch and he joined her. "Hey. What are you doing up here?"

"Looking. It's beautiful." She grinned.

"I guess it is. I still don't understand why you're here." He sat down next to her. "There isn't much point just looking."

"We ought to go down." Otto said after about five minutes. They both climbed down quickly and pulled their back packs on. The eight of them started back up the mountain. They walked for most of that day and the next. At about three o'clock in the afternoon on their second day of walking they found a small lake or large pond, depending on one's point of view. Kati was the one to suggest that they stay put. It was particularly hot that day and none of them really wanted to keep going. They set up the tents quickly and relaxed in the shade. Otto and Alcester were the first to be tempted by the cool water of the lake. They stripped down to boxers and jumped in, splashing each other and acting like children. It wasn't long before Kati joined them. She 'accidently' splashed Khan who was more than willing to get revenge on her. Soon only Jade and Sophia were sitting on the edge.

Otto swam over to them. "Aren't you going to join in?" He asked, slightly out of breath.

"No, I didn't bring my swimming costume." Sophia said without opening her eyes. "Anyway, it's nice here."

"No-one else has swimming stuff." He pointed out.

"I know." She opened one eye just in time to see Otto splash her. She gasped in surprise and stood up, soaking wet and grinning. "You are so dead." She quickly pulled off her top and shorts, they were dripping, and dived into the water. Otto was already swimming away from her. She heard Jade jump in a few moments later. After several minutes trying to catch up with Otto she gave up and floated on her back until he realised that she wasn't following him and swam back towards her. He got close and she flipped over, dove under and grabbed his ankle.

He slipped out of her grasp and she came up and was splashed in the face. She spluttered in surprise and glowered at Otto as he laughed. She splashed him back and he grabbed her around the waist. She shrieked as he lifted her and threw her as far as he could while treading water. Sophia came down and went under. She swam back to him underwater. She came up right next to him, grinning. His arms wrapped around her and her breath caught. She suddenly became very aware that they were both dressed in only their undergarments. A slight blush crept over her cheeks. Otto smiled at her as she slipped her arms around his neck. Suddenly a large volume of water caught them both in the face. Sophia smiled at him and turned to see their attackers. Alcester and Kati were grinning at them. Otto shot her a look and they took off after the other two.

* * *

So Sophia is bonding with the augments.

Thank you for all the reviews. I love knowing what you think. Please put down any ideas you have.


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